########################################################################### # Things to do # # ########################################################################### # This is the qatest.dat file that is used by scripts/qatest.pl # # The script should be run from the directory test/qa # # Additional input data is expected to be found in the directory test/data # # If no argument is given to the script it will run through all of the # entries in this file. If an argument is supplied it will search for # the entry whose ID name matches the argument and will run that one. # # To run the script and retain the files created during the test, use # ../../scripts/qatest.pl key:-kk # # The results of the QA tests will be stored in the file # test/qa/qatest.log # # Typical example entry for an EMBOSS package program (AP line) # See below for AA/AB (EMBASSY) and AQ (make check) entries # # ID programname-ex (the ID name of this test) # UC text (not used in the QA test - used in the HTML documentation) # AP programname (the name of the application to test) # CL (the command-line arguments to use after the application name) # IN (a response to a prompt for input using the default) # IN text (a response to a prompt using a non-default input) # IK text (input keystrokes, not responses to prompts) # FI filename (an expected output filename) # FZ integer (the expected size in bytes of the above filename) # FC integer (the expected number of lines in the above file) # FP /regexp/ (an expected perl regular expression in the above file) # FP integer /regexp/ (a regexp that is expected integer number of times) # FI stderr (these are standard checks on the expected error reports) # FC = 2 # FP 0 /Warning: / # FP 0 /Error: / # FP 0 /Died: / # // (marks the end of the entry) # # ID identifier # The identifier is formed from the name of the application being # tested and a tag to indicate what sort of test is being performed. # The identifier is used to create a directory test/qa/. # Typical tags are: # -ex = example used to create the HTML documentation # -ex2, -ex3 = further examples used in the documentation # In general, all documentation examples should have tests # to check the documentation is correct. # -keep If the test has a "DL keep" line the resulting files are kept. # Used for database indexing - later tests will use the results! # -fail Testing a failure condition (ER line) # AA Application name for an EMBASSY package application. # This is used for the command line and for reporting statistics. # The application must be built by "make" for the EMBASSY package # defined in the AB line for this test definition. # If the application is not found, qatest can assume this # EMBASSY package was not installed. # AB EMBASSY package name # Used to inform the qatest script that a test depends on # installation of an EMBASSY package and may fail to find the binary. # AP Application name for EMBOSS application # This is used for the command line and for reporting statistics. # The application must be a standard EMBOSS application, built by make. # The test must succeed. # AQ Application name for "make check" application # This is used for the command line and for reporting statistics. # The application must be built by "make check". # The qatest script will look in the build directory as this # application will not be installed. # If the application is not found, qatest can assume "make # check" was not run. # CC Comment # Used in commenting on failed tests # This comment will appear in the test output on failure as a guide # to an acceptable failure condition (check the error message too!) # See ## lines for general comments within the definition # CL Command line # (Optional) # This is the rest of the command line. # Multiple CL lines are appended with a space in between. # DI Directory # Name of a directory created in the results directory # No tests currently for the contents, but a QQ postprocessing # command could be used to list the contents to another file. # DL 'success' or 'all' or 'keep' # (Optional) # 'success' = delete the test directory on success (the default) # 'all' = delete the test directory always # 'keep' = keep the test results directory always # (used if another test reuses the results, # e.g. database indexing) # ER error return code # (Optional) # Error code expected. # Used for tests that are test failure conditions. # The test reports an error if the error code is not found # FC [<=>] number # = nn Number of lines # > nn More than nn lines # < nn Less than nn lines # FI File name # (Required for all output files created) # stdout and stderr are assumed to exist and be empty unless stated. # FP File pattern # (Required for all non stdout and stderr files) # perl /regexp/ to be found in the preceeding 'FI' file. # The /regexp/ may be preceded by an optional count to check exact # number. # As an extra check, stderr (which often contains the user prompts) # should be checked for absence of warning, error and died messages. # FZ [<=>] number # (Required for all non stdout and stderr files) # File size test on the preceeding 'FI' file. # The file size may be qualified with an optional relation '=', '>' etc. # Implicit test for zero size stdout/stderr unless stated. # IC text # (Optional) # This information is not used in the QA testing. # It is used by scripts/makeexample.pl when creating the HTML # documentation files to annotate the input. # IN Line input # (Required for each prompted input) # If there is nothing on the line, then an empty line is input to the # application. (Obvious really, but needs to be said) # Care is needed if standard options are added/removed from the program. # OC text # (Optional) # This information is not used in the QA testing. # It is used by scripts/makeexample.pl when creating the HTML # documentation files to annotate the output. # PP Preprocessor command # (Optional) # Command executed (by /bin/sh) before the test. # Each PP line is a separate command. Long lines are not concatenated. # e.g. Set an environment variable required by the application. # The variable should always be exported (this is /bin/sh), for example: # PP EMBOSS_ACDROOT=../../acd # PP export EMBOSS_ACDROOT # QQ Postprocessor command # (Optional) # Command executed (by /bin/sh) after the test. # Each QQ line is a separate command. Long lines are not concatenated. # Not used at present. Most likely application is to list the # contents of a directory to another file, which can then be # tested for size and patterns. # RQ required # Required external programs. For example, srs for tests that # use getz, or clustalw for emma # TI seconds # Timeout for test. The default is 60 seconds. Some examples # can take longer on a heavily loaded system. # UC text # (Optional) # This information is not used in the QA testing. # It is used by scripts/makeexample.pl when creating the HTML # documentation files to annotate the examples of usage. # ## Comment # (Optional) # This is a comment. # Double # is required. # This is only a comment in the entry and is not reported # (use CC lines for comments that appear on failure) #################### # Command line tests #################### ID acdc-0001 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0002 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -aint 5 -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0003 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -ai 5 -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0004 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 -sbegin 5 -send 1000 tembl:x13776 x.x -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0005 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 -sbegin 5 -send 1000 x.x -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0006 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest -sbegin 5 -send 1000 tembl:x13776 tembl:x13776 x.x -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0007 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -sbegin 5 -send 1000 -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0008 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x CL -sbegin_asequence 5 -send_asequence 1000 -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0009 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -sbegin_as 5 -send_as 1000 -auto FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 // ID acdc-0010 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest -help FI stderr FZ = 1391 FP /^Version: EMBOSS:6\.\d+\.[\d.]+\n/ FP 3 / qualifiers:\n/ FP 4 / qualifiers:/ FP 1 /^ +\[-asequence\] +sequence +Sequence filename and optional format, or\n/ FP 1 /^ +\[-bsequence\] +sequence +Sequence filename and optional format, or\n/ FP 2 /^ +\[-[a-z]sequence\] +sequence +Sequence filename and optional format, or\n/ FP / [-]testalen string asequence length \.\.\./ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdc-0011 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest -help -verbose FI stderr FZ = 4496 FP /^Version: EMBOSS:6\.\d+\.[\d+.]+\n/ FP 27 / boolean / FP 7 / integer / FP 26 / string / FP / [-]testalen string asequence length \.\.\./ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdc-0012 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -debug IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x.x FZ = 0 FI x13776.fasta FZ = 0 FI x13776.out2 FZ = 0 FI qatest.dbg FP /seqinUsaProcess 'tembl:x13776'/ FP 0 /^Memory usage / // ID acdc-ex AP acdc CL antigenic IN tsw:actb1_takru IN IN FI actb1_takru.antigenic FZ = 0 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdlog-check AQ acdlog CL antigenic IN tsw:actb1_takru IN IN FI actb1_takru.antigenic FZ = 0 FI antigenic.acdlog FC = 5685 FP 51 /^acdProcess/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdpretty-ex AP acdpretty PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest FI qatest.acdpretty FZ = 847 FP 2 /[\#]/ FP 3 /^string:/ FP 12 /^[a-z]+: / FI stdout FC = 1 FP /^Created qatest\.acdpretty\n/ // ID acdrelations-ex AQ acdrelations PP mkdir ./acdfiles PP cp ../../../emboss/acd/antigenic.acd ./acdfiles QQ rm -rf ./acdfiles CL -intypefile ../../../emboss/acd/knowntypes.standard IN IN acdfiles IN . FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI antigenic.acd FC = 50 FP 5 /relations: / // ID acdtable-ex AP acdtable CL antigenic FI stderr FC = 54 FP 9 /[<]tr/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdtrace-ex AP acdtrace CL antigenic IN tsw:actb1_takru IN IN FI actb1_takru.antigenic FZ = 0 FI stderr FC = 20 FP 9 /^Trace: +\d+/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acdvalid-ex AP acdvalid CL antigenic FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // #################### # ACD parsing errors #################### ID acd-nofile AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL nofile FI stderr FZ > 0 FP /Error: File \.\.[\/\\]\.\.[\/\\]acd[\/\\]nofile\.acd line 0: ACD file not opened\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noappl AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noappl FI stderr FZ > 0 FP /Error: File .*noappl\.acd line 4: Application definition required at start\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-secondappl AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL secondappl FI stderr FZ > 0 FP /Error: File .*secondappl\.acd line 9: Application definition allowed only at start\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noleftq AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noleftq FI stderr FZ > 0 FP /Error: File .*noleftq\.acd line 7: \(output\) Failed to find '\[' for section output\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noleftsec AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noleftsec FI stderr FZ > 0 FP /Error: File .*noleftsec\.acd line 5: \(output\) Failed to find '\[' for section output\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noleftappl AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noleftappl FI stderr FZ > 0 FP /Error: File .*noleftappl\.acd line 3: \(noleftappl\) Failed to find '\[' for application noleftappl\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acd-noendsec AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noendsec FI stderr FZ > 0 FP /Error: Section 'output' has no endsection\n/ FP /Error: Section 'input' has no endsection\n/ FP 2 /Error: Section '[a-z]*' has no endsection\n/ FP /Error: File .*noendsec\.acd line 13: Unclosed sections in ACD file\n/ FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / // ID acd-noquote AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noquote FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noquote\.acd line 5: \(outtest\) Unexpected end of file, no closing quote\n/ // ID acd-novalue AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL novalue FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*novalue\.acd line 5: \(outtest\) Unexpected end of file, attribute value not found\n/ // ID acd-badstage AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badstage FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badstage\.acd line 5: Unrecognized token 'dingsbum'\n/ // ID acd-calcparam AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL calcparam FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*calcparam\.acd line 22: [(]outtest[)] 'parameter' attribute cannot use a variable\. It is used .* been set\n/ // ID acd-noapplname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noapplname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noapplname\.acd line 3: Bad or missing application name '\['\n/ // ID acd-badapplname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badapplname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badapplname\.acd line 3: Bad or missing application name 'run[*]123'\n/ // ID acd-noqualname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noqualname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noqualname\.acd line 5: Bad or missing qualifier alphabetic name '\['\n/ // ID acd-badqualname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badqualname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badqualname\.acd line 5: Bad or missing qualifier alphabetic name 'sequence1'\n/ // ID acd-badalias AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badalias FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badalias\.acd line 5: Bad syntax qualifier alias name 'file2'\n/ // ID acd-nocolon AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL nocolon FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*nocolon\.acd line 5: Expected ':' not found after 'param'\n/ // ID acd-badendsec AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL badendsec FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*badendsec\.acd line 14: Bad endsection 'fred', current section is 'output'\n/ // ID acd-endsecextra AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL endsecextra FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*endsecextra\.acd line 18: Bad endsection 'fred', not in a section\n/ // ID acd-dupname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupname\.acd line 14: \(outtest\) Name 'outtest' not unique\n/ // ID acd-dupalias AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupalias FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupalias\.acd line 14: \(output\) Name\/Alias 'outtest'\/'output' not unique\n/ // ID acd-ambigtype AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigtype FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*ambigtype\.acd line 16: ambiguous acd type seqo \(seqout,seqoutall,seqoutset\)\n/ // ID acd-ambigvar AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigvar tembl:x13776 -auto FI stderr FZ > 0 FP 1 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*ambigvar\.acd line 9: Failed to resolve variable 'seq'\n/ FP /Warning: ambiguous item seq \(sequence,seqmod\)\n/ // ID acd-undefvar AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL undefvar tembl:x13776 -auto FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*undefvar\.acd line 7: Variable 'seqmod' not yet defined\n/ // ID acd-leftend AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL leftend FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*leftend\.acd line 5: \(outtest\) End of file looking for '\]'\n/ // ID acd-valend AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL valend FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*valend\.acd\ line 5: \(outtest\) End of file looking for '\]'\n/ // ID acd-noattname AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL noattname FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*noattname\.acd line 5: \(outtest\) Bad or missing attribute name 'requ1red'\n/ // ID acd-dupassoc AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupassoc FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupassoc\.acd line 5: \(sbegin\) Associated qualifier 'sbegin' clashes with 'sbegin' in ACD file\n/ // ID acd-dupassocb AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL dupassocb FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*dupassocb\.acd line 5: \(mybool\) Associated qualifier 'sbegin' clashes with 'mybool'\/'sbegin' in ACD file\n/ // ID acd-wrongattr AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL wrongattr FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Error: File .*wrongattr\.acd line 7: \(outtest\) Attribute 'wanted' unknown\n/ // ID acd-ambigdefattr AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigdefattr tembl:x13776 -filter FI stderr FZ > 0 FP 1 /Warning: Ambiguous name/token 'd' \(debug,die\)/ FP 1 /Error: / FP 0 /Died: / FP /Error: File .*ambigdefattr\.acd line 3: \(ambigdefattr\) Attribute or qualifier 'd' ambiguous \(debug,die\)\n/ // ID acd-ambigassoc AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL ambigassoc FI stderr FZ > 0 FP 1 /Warning: / FP 1 /Error: / FP 0 /Died: / FP /Warning: Ambiguous name/token 'f' \(fformat,fopenfile\)\n/ FP /Error: File .*ambigassoc\.acd line 8: \(asequence\) Attribute or qualifier 'f' ambiguous \(fformat,fopenfile\)\n/ // ID acd-mixedcase AP acdpretty PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL mixedcase FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: File .*mixedcase\.acd line 16: Automatically converting 'testA' to lower case\n/ FI mixedcase.acdpretty FZ > 0 FP /: testa / FI stdout FC = 1 FP /Created mixedcase\.acdpretty\n/ // ID acd-testarray AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testarray FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP 1 /^Error: .*testarray\.acd line 8: \(numlist\) Array attribute size: 0 less than 1/ // ID acd-attralias AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalias FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FP 1 /^Error: .*testalias\.acd line 22: \(hstring\) Attribute 'requ' unknown/ // ## Command line validation tests ## Handling of associated qualifiers ID acdc-badqual AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testassoc tembl:v00294 tembl:x13776 -sbegin_a 10 IN IN FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Warning: Ambiguous master qualifier 'a' in sbegin_a \(auto,asequence,atest\)/ FP /Died: Unknown qualifier -sbegin_a/ // ID acdc-ambigqual AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -a 5 -auto ER 1 FI stderr FP 1 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Warning: ambiguous qualifier 'a' \(auto,asequence,aint\)/ FP /Died: Unknown qualifier -a\n/ // ID acdc-missing AP acdc ## "" as a parameter is a missing value treated as an empty string PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 "" x.x ER 1 FI stderr FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Unable to read sequence ''\n/ FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/ // ID acdc-missing2 AP acdc ## "" as a qualifier value is a missing value treated as an empty string PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 -bsequence="" x.x ER 1 FI stderr FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Unable to read sequence ''\n/ FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/ // ID acdc-missing3 AP acdc ## Empty qualifier value is a missing value treated as an empty string PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 -bsequence= x.x ER 1 FI stderr FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Unable to read sequence ''\n/ FP /Died: qatest terminated: Bad value for '-bsequence' and no prompt\n/ // ID acdc-noprefixvalue AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -auto -nologic=Y ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: 'no' prefix used with value for '-nologic=Y'\n/ // ID acdc-noprefixbad AP acdc ## no nullok attribute for this type PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -auto -nooutdir ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: 'no' prefix invalid for '-nooutdir'\n/ // ID acdc-noprefixbad2 AP acdc ## nullok attribute is false PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -auto -notestalen ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: 'no' prefix invalid for '-notestalen'\n/ // ID acdc-novalue AP acdc ## nullok attribute is false PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -auto -testalen ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: Value required for '-testalen'\n/ // ID acdc-novalue2 AP acdc ## nullok attribute is false PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatest tembl:x13776 tembl:x13776 x.x -auto -testalen -testblen ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: Value required for '-testalen' before '-testblen'\n/ // ID acdc-codebad AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_LANGUAGE=bad PP export EMBOSS_LANGUAGE CL qatest -help ER 1 FI stderr FP 0 /Warning: / FP 0 /Error: / FP 1 /Died: / FP /Died: Bad format in codes file \.\.[\/\\]\.\.[\/\\]acd[\/\\]codes\.bad after 'defbool "Yes or No"'\n/ // ID acdc-codemissing AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_LANGUAGE=missing PP export EMBOSS_LANGUAGE CL qatest -help FI stderr FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: Code file \.\.[\/\\]\.\.[\/\\]acd[\/\\]codes\.missing not found\n/ // ID acdc-testassoc AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testassoc tembl:v00294 tembl:x13776 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 1113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc2 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send at the start should work on both sequences CL testassoc -send -1001 tembl:v00294 tembl:x13776 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 1167:/ // ID acdc-testassoc3 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send after first sequence should work on first sequence CL testassoc tembl:v00294 -send -1001 tembl:x13776 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc4 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send after second sequence should work on second sequence CL testassoc tembl:v00294 tembl:x13776 -send -1001 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 1113:/ FP /Bsequence end 1167:/ // ID acdc-testassoc5 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## -send after another qualifier should work on all sequences CL testassoc tembl:v00294 tembl:x13776 -ctest "fred" -send -1001 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 1167:/ // ID acdc-testassoc6 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -send for first sequence CL testassoc tembl:v00294 tembl:x13776 -ctest "fred" -send1 -1001 IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc7 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -send for first sequence CL testassoc -send1 -1001 tembl:v00294 tembl:x13776 -ctest "fred" IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc8 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -send for first sequence CL testassoc tembl:v00294 tembl:x13776 -send1 -1001 -ctest "fred" IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 2167:/ // ID acdc-testassoc9 AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -sformat for first sequence makes -send global CL testassoc tembl:v00294 tembl:x13776 -sformat1 embl -send -1001 -ctest "fred" IN IN FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Asequence end 113:/ FP /Bsequence end 1167:/ // ID acdc-toomanyparam AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT ## Numbered -sformat for first sequence makes -send global CL testassoc tembl:v00294 tembl:x13776 tembl:k00650 IN IN FI stderr FZ > 0 FP /^Error: Argument 'tembl:k00650' : Too many parameters 3\/2\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / // ID acdc-alignbadformat AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalign -aformat fred IN FI stderr FZ > 0 FP /Error: Unknown alignment format 'fred'\n/ FP /Died: Alignment option -atest: Validation failed\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-alignbadminseq AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalign IN FI stderr FZ > 0 FP /Error: Alignment format pair specifies at least 2 sequences, alignment has only 0\n/ FP /Died: Alignment option -atest: Validation failed\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-alignbadmaxseq AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalignpair IN FI stderr FZ > 0 FP /Error: Alignment format pair specifies at most 2 sequences, alignment has 3\n/ FP /Died: Alignment option -atest: Validation failed\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-alignbadwidth AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testalignok -awidth 9 IN FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: Alignment width \(-awidth=9\) too narrow, reset to 10\n/ FI outfile.testalignok FZ = 0 // ID acdc-funconeof AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL oneof IN thr IN 2 FI stderr FZ > 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP / Pick a number / // ID acdc-funconeoffalse AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL oneof IN two FI stderr FZ > 0 FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Warning: integer value out of range 0 less than \(reset to\) 1\n/ // ID acdc-nodatafile AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL datafile -pepdatafile badname.dat IN FI stderr FZ > 0 FP /Error: Unable to open data file 'badname\.dat' for input\n/ FP /Died: datafile terminated: Bad value for '-pepdatafile' and no prompt\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID acdc-listambig1 AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN f FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: 'f' is ambiguous \(fa,four,fb,five\)\n/ FP /Error: Bad menu option 'f'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-listambig2 AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN t FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: 't' is ambiguous \(two,three\)\n/ FP /Error: Bad menu option 't'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-listbad AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN x FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: 'x' is not a valid menu option\n/ FP /Error: Bad menu option 'x'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ FP /Accepted short codes are: a,b,c,fa,fb\n/ // ID acdc-listmax AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN a,b,c,four FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: Menu allows no more than 3 values\n/ FP /Error: Bad menu option 'a,b,c,four'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-listmin AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testlist IN FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: Menu needs 1 value\n/ FP /Error: Bad menu option ''\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-reportbadformat AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testreport -rformat fred IN FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Unknown report format 'fred'\n/ FP /Died: Report option -rtest: Validation failed\n/ // ID acdc-reportbadtaglist AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testreporttags IN FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /Error: Bad report taglist at ' str s=String'\n/ FP /Error: File .*testreporttags\.acd line 8: \(rtest\) Bad tag list for report\n/ // ID acdc-selectambig AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN f FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: 'f' is ambiguous \(four,five\)\n/ FP /Error: Bad select option 'f'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-selectbad AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN x FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: 'x' is not a valid selection list option\n/ FP /Error: Bad select option 'x'\n/ FP /Accepted values are: one,two,three,four,five\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-selectmax AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN one,two,thr,four FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: Selection list allows no more than 3 values\n/ FP /Error: Bad select option 'one,two,thr,four'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-selectmax2 AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN 1,2,3,4 FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: Selection list allows no more than 3 values\n/ FP /Error: Bad select option '1,2,3,4'\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-selectmin AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL testselect IN FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FP /Error: Selection list needs 1 value\n/ FP /Error: Bad select option ''\n/ FP /Error: Unable to get reply from user - end of standard input\n/ // ID acdc-retry AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_ACDPROMPTS=2 PP export EMBOSS_ACDPROMPTS CL testselect IN 6 IN 7 FI stderr FZ > 0 FP 0 /Warning: / FP 4 /Error: / FP 1 /Died: / FP 2 /Error: Bad select option '[1-9]'\n/ FP /Died: testselect terminated: Bad value for '-stest' and no more retries\n/ // ID acdc-badadvanced AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_ACDPROMPTS=2 PP export EMBOSS_ACDPROMPTS CL testselect -numtest fred IN 5 FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: Invalid integer value 'fred'\n/ FP /Died: testselect terminated: Bad value for '-numtest' and no prompt\n/ // ID acdc-badauto AP acdc ER 1 PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT PP EMBOSS_ACDPROMPTS=2 PP export EMBOSS_ACDPROMPTS CL testselect -stest 6 -auto FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP 1 /Error: Bad select option '[1-9]'\n/ FP /Died: testselect terminated: Bad value for '-stest' with -auto defined\n/ // ########################## # .embossrc parsing errors ########################## ID nam-badsummary AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badsummary.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 1 /Died: / FP /Error: File .*\.embossrc line 2: Error\(s\) found in included file [$]emboss_badfile \(\.\.[\/\\]\.\.[\/\\]rc[\/\\]badsummary.rc\)\n/ FP /Died: Error\(s\) in configuration files\n/ // ID nam-badtype AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badtype.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 3 /Error: / FP 1 /Died: / FP /Error: File .*badtype\.rc line 1: Invalid definition type 'this'\n/ FP /Error: File .*badtype\.rc line 1: Invalid definition type 'badtype'\n/ FP /Error: File .*\.embossrc line 2: Error\(s\) found in included file [$]emboss_badfile \(\.\.[\/\\]\.\.[\/\\]rc[\/\\]badtype.rc\)\n/ // ID nam-badset AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badset.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*badset\.rc line 7: Unexpected end of file in SET definition\n/ // ID nam-baddb AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/baddb.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*baddb\.rc line 3: Unexpected end of file in DBNAME definition\n/ // ID nam-badresattr AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badresattr.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*badresattr\.rc line 3: Bad attribute 'badattr' for resource 'badresource'\n/ // ID nam-badinclude AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/badinclude.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / FP /Error: File .*\.embossrc line 2: Failed to open include file '[$]emboss_badfile'/ // ID nam-includeagain AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/includeagain.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*includeagain\.rc line 3: [$]emboss_badfile \(\S+\) already read \.\.\. skipping\n/ // ID nam-dbempty AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/dbempty.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 5 /Error: / FP 1 /Died: / FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no attributes\n/ FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no format definition\n/ FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no type definition\n/ FP /Error: File .*dbempty\.rc line 3: Database 'empty' has no access method definition\n/ // ID nam-dbunknowns AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/dbunknowns.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 4 /Error: / FP 1 /Died: / FP /Error: File .*dbunknowns\.rc line 4: Database 'unknowns' format: 'noformat' unknown\n/ FP /Error: File .*dbunknowns\.rc line 4: Database 'unknowns' method: 'notknown' unknown\n/ FP /Error: File .*dbunknowns\.rc line 4: Database 'unknowns' type: 'nosuchtype' unknown\n/ // ID nam-rsempty AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/rsempty.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /Error: File .*rsempty\.rc line 3: Resource 'empty' has no attributes\n/ // ID nam-dbnoquote AP showdb ER 1 PP EMBOSSRC=../../rc PP export EMBOSSRC PP EMBOSS_BADFILE=../../rc/dbnoquote.rc PP export EMBOSS_BADFILE FI stderr FZ > 0 FP 0 /Warning: / FP 4 /Error: / FP 1 /Died: / FP /Error: File .*dbnoquote\.rc line 4: '\]' found, unclosed quotes in 'unclosed single quotes'\n/ FP /Error: File .*dbnoquote\.rc line 8: '\]' found, unclosed quotes in 'unclosed double quotes'\n/ FP /Error: File .*dbnoquote\.rc line 12: '\]' found, unclosed quotes in 'unclosed mixed quotes''\n/ // ####################### # Associated qualifiers ####################### ID qual-ufo AP seqret CL ../../data/hba.fa -feat -ufo ../../data/hba.gff CL -auto -sf fasta FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI hba_human.fasta FC = 4 FP /^>HBA_HUMAN / FI hba_human.gff FC = 161 FP /^##gff-version 3\n/ FP /^#!Type Protein\n/ FP /^##sequence-region HBA_HUMAN 1 141\n/ // ID qual-ufo-noid AP seqret CL ../../data/noid.fa -feat -ufo ../../data/noid.gff -sid HBA_HUMAN -sprot CL -stdout -auto -sf fasta FI stderr ## GFF output truncated to match the length of the input sequence ## Type DNA because the input sequence is. FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>HBA_HUMAN/ FI stdout.gff FC = 28 FP /^##gff-version 3\n/ FP /^#!Type Protein\n/ FP /^##sequence-region HBA_HUMAN 1 19\n/ FP 2 /^HBA_HUMAN\tSWISSPROT\tnatural_variant\t19\t19\t/ FP 0 /^HBA_HUMAN\tSWISSPROT\tnatural_variant\t20\t20\t/ FP /\tID=HBA_HUMAN.4;note=ACETYLATION;comment=IN VARIANT THION/ FP /THIONVILLE%3B WHERE THE INITIATOR MET IS NOT CLEAVED\n/ // ID qual-sid AP seqret CL ../../data/noid.fa CL -stdout -auto -sf fasta -sid fred ## Fails to use -sid in the output FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>fred/ // ID qual-sid2 AP seqret CL ../../data/noid.fa CL -stdout -auto -sf fasta -sid fred -osf ncbi ## Fails to use -sid in the output FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^>gnl\|unk\|fred/ // ID qual-sdb AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -sdb fred ## noid.fa has no sequence ID ## This upsets the feature reading ## Error GFF Group field for table '' FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>HBA_HUMAN/ // ID qual-sdb2 AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -sdb fred -osf ncbi ## noid.fa has no sequence ID ## This upsets the feature reading ## Error GFF Group field for table '' FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>gnl[|]fred[|]HBA_HUMAN / // ID qual-osdb AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -osdb fred FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>fred:HBA_HUMAN / // ID qual-osdb2 AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -osdb fred -osf ncbi FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>gnl[|]fred[|]HBA_HUMAN / // ID qual-osdb3 AP seqret CL ../../data/hba.fa CL -stdout -auto -sf fasta -sdb jim -osdb fred -osf ncbi FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^>gnl[|]fred[|]HBA_HUMAN / // ############################################################### # # DAS sequence/feature access methods # ############################################################### ID cachedas-ex TI 300 AP cachedas CL -servername tdas -auto CL -cachefile ~/.embossdata/qatests.server.dasregistry QQ cp ~/.embossdata/qatests.server.dasregistry . FI qatests.server.dasregistry FP 1 /^DB uniprot / FI stdout FC > 30 FP /embl/ // ID dasregistry-noseqsupport AP seqret CL tdas:BacAbs:Q7DDU3 -sbegin 1 -send 10 stdout -auto ER 1 FI stderr FC > 2 FP 1 /no match to query type 'sequence'/ FP 1 /Died: / // ID dasregistry-featquery AP featcopy CL tdas:cath:5pti stdout -auto FI stdout FP 1 /inferred from structural similarity/ // ID dasregistry-featquery-range AP featcopy CL tdas:Homo_sapiens_GRCh37_transcript:10[32889611:32973347] stdout -auto FI stdout FP 2 /Target=ENST00000375030/ FP 2 /Target=ENST00000375028/ FP 1 /Target=ENST00000422668/ // ID dasregistry-featquery-type AP featcopy CL "tdas:Homo_sapiens_GRCh37_reference-{segment:11 & type:supercontig}" stdout -auto FI stdout FP 4 /supercontig/ // ID dasregistry-uniprot AP seqret CL tdas:uniprot:P00280 -sbegin 1 -send 10 stdout -auto FI stdout FC = 2 FP 1 /^>P00280/ FP 1 /MLAKATLAIV/ // ID dasregistry-uniprot-multipleseqs AP seqret CL "tdas:uniprot:{P00280, p12344}" stdout -auto FI stdout FC = 13 FP 1 /^>P00280/ FP 1 /MLAKATLAIV/ FP 1 /^>P12344/ FP 1 /MALLHSGRFL/ // ID dasregistry-uniparc AP seqret CL tdas:uniparc:UPI000000000A -sbegin 1 -send 10 stdout -auto FI stdout FC = 2 FP 1 /^>UPI000000000A_1,10/ FP 1 /MAETKEFKTL/ // ID das-genedas AP seqret CL tgenedashuman:ENSG00000139618 -send 10 stdout -auto FI stdout FC = 2 FP 1 /^>ENSG00000139618/ FP 1 /^gggcttgtgg/ // ID das-ensembldasgrch37 AP seqret CL tensembldasgrch37:11 -sbegin 60001 -send 60010 stdout -auto FI stdout FC = 2 FP 1 /^>11_60001,60010/ FP 1 /^gaattctaca/ // ID cachedas-ensembl AP cachedas TI 300 CL -servername tensembldasserver -auto CL -cachefile ~/.embossdata/qatests.server.ensembldasserver QQ cp ~/.embossdata/qatests.server.ensembldasserver . FI qatests.server.ensembldasserver FP /^DB Ailuropoda_melanoleuca/ FI stdout FC > 30 FP /embl/ // ID das-ensembldasservergrch37 ## same as above test (das-ensembldasgrch37), ## using tensembldasserver based DB instead of directly defined dassource DB AP seqret CL tensembldasserver:Homo_sapiens_GRCh37_reference:11 CL -sbegin 60001 -send 60010 stdout -auto FI stdout FC = 2 FP 1 /^>11_60001,60010/ FP 1 /^gaattctaca/ // ############################################################### # # EBI webservices # ############################################################### ID cachedbfetch-wsdbfetch RQ soapws CC requires (axis2C) SOAP webservices library enabled CC this test can be disabled using -without=soapws option AP cachedbfetch CL -servername twsdbfetch -auto CL -cachefile ~/.embossdata/qatests.server.twsdbfetch QQ cp ~/.embossdata/qatests.server.twsdbfetch . FI qatests.server.twsdbfetch FP 1 /^DB uniprotkb / FP /embl/ FI stderr FC < 140 // ID cachedbfetch-ex AP cachedbfetch CL -servername tdbfetch -auto CL -cachefile ~/.embossdata/qatests.server.tdbfetch QQ cp ~/.embossdata/qatests.server.tdbfetch . FI qatests.server.tdbfetch FP 1 /^DB uniprotkb / FP /embl/ FI stderr FC < 140 // ID wsdbfetch-uniprot TI 120 RQ soapws CC requires (axis2C) SOAP webservices library enabled AP seqret CL fasta::twsdbfetch:uniprotkb:P06213 stdout -auto FI stdout FC = 25 FP 1 /^>INSR_HUMAN/ FP 1 /PS$/ // ID dbfetch-uniprot AP seqret CL fasta::tdbfetch:uniprotkb:P06213 stdout -auto FI stdout FC = 25 FP 1 /^>INSR_HUMAN/ FP 1 /PS$/ // ID wsdbfetch-edam RQ soapws CC requires (axis2C) SOAP webservices library enabled AP ontoget CL twsdbfetch:edam:0000352 stdout -auto FI stdout FC > 10 FP /local alignment/ // ID dbfetch-edam AP ontoget CL tdbfetch:edam:0000352 stdout -auto FI stdout FC > 10 FP /local alignment/ // ID wsdbfetch-uniprotxml RQ soapws CC requires (axis2C) SOAP webservices library enabled AP textget CL uniprotxml::twsdbfetch:uniprotkb:p12345 stdout -auto FI stdout FC > 160 FP 1 /P12345/ // ID dbfetch-uniprotxml AP textget CL uniprotxml::tdbfetch:uniprotkb:p12345 stdout -auto FI stdout FC > 160 FP 1 /P12345/ // ID wsdbfetch-noentry RQ soapws TI 120 CC requires (axis2C) SOAP webservices library enabled AP seqret CL fasta::twsdbfetch:uniprotkb:abcdefg stdout -auto ER 1 FI stderr FC = 2 FP 1 /Unable to read sequence/ // ID dbfetch-noentry AP seqret CL tdbfetch:uniprotkb:abcdefg stdout -auto ER 1 FI stderr FC = 2 FP 1 /Unable to read sequence/ // ID cacheebeyesearch-ex RQ soapws TI 180 CC requires (axis2C) SOAP webservices library enabled AP cacheebeyesearch CL -cachefile ~/.embossdata/qatests.server.ebeye -auto QQ cp ~/.embossdata/qatests.server.ebeye . FI qatests.server.ebeye FP 1 /^DB uniprot / // ID ebeye-uniprot RQ soapws CC requires (axis2C) SOAP webservices library enabled AP textget CL tebeye:uniprot:1A74_HUMAN stdout -auto FI stdout FC > 10 FP /P30459/ FP /histocompatibility antigen/ // ID ebeye-emblrel_con-multifield RQ soapws CC requires (axis2C) SOAP webservices library enabled AP textget CL "tebeye:emblrelease_con-{keywords:Aspergillus fumigatus & description:BAC}" CL stdout -auto FI stdout FP /BX649216/ FP /Aspergillus fumigatus BAC pilot project supercontig/ // ID ebeye-uniprot-multifield RQ soapws CC requires (axis2C) SOAP webservices library enabled AP textget CL "ebeye:uniprot-{description:genome polyprotein & sequence_length:496}" CL stdout -auto FI stdout FP /B8LSD5/ FP /Genome polyprotein/ FP /seq.*length.*496/ FP /emblcds: ABV55385/ // ################### # Ensembl ################### ID cacheensembl-ex TI 180 AP cacheensembl CL -servername ensembl -cachefile ~/.embossdata/qatests.server.ensembl -auto QQ cp ~/.embossdata/qatests.server.ensembl . FI qatests.server.ensembl FP 1 /^ALIAS 9606 homo_sapiens\n/ FP 9 /^ALIAS \S+ homo_sapiens\n/ FP 1 /^DBNAME homo_sapiens \[/ FP 6 /^DBNAME homo_sapiens/ FI stdout FC = 125 FP 6 /homo_sapiens/ // ################### # Main applications ################### ID aaindexextract-keep AP aaindexextract DL keep PP mkdir ./AAINDEX PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/aaindex1.test FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI AAINDEX DF kytj820101 // ID abiview-ex AP abiview CL -graph cps IN ../../data/abiview.abi IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created abiview\.ps\n/ FI abiview.fasta FP /^>abiview\n/ FP /^GNNNNNNNNNG/ FZ = 861 FI abiview.ps FP /^%%Title: PLplot Graph\n/ // ##ID abiview-old ##AP abiview ##CC Example file missing test/data/ba16d2.s1 ##CL -graph ps ##IN ../../data/ba16d2.s1 ##IN ##FI stderr ##FC = 2 ##FI stdout ##FZ = 18 ##FP /^Created abiview\.ps\n/ ##FI outfile.fasta ##FZ = 0 ##// ID aligncopy-ex AP aligncopy IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.aligncopy FC = 68 FP /HBB_HUMAN 1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR 40\n/ FP / :: : : :.: : : : :::: :: : : : : \n/ // ID aligncopypair-ex AP aligncopypair IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.aligncopypair FC = 683 FP 21 /Aligned_sequences:/ FP /HBB_HUMAN 1 --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQR 40\n/ // ID antigenic-command AP antigenic CL tsw:amir_pseae -auto FI amir_pseae.antigenic FP /^# Program: antigenic\n/ FP /Sequence: AMIR_PSEAE/ FP /246/ FP /1\.246/ FP / NSLLGSL/ FZ > 100 FC > 5 // ID antigenic-ex AP antigenic IN tsw:actb1_takru IN IN FI actb1_takru.antigenic FP /^# Program: antigenic\n/ FP /1\.207/ FP /AA[^AV]VV/ FZ > 100 FC > 5 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID antigenic-ex2 UC By using the '-rformat gff' qualifier, a GFF file of the predicted regions can be produced. AP antigenic CL -rformat gff IN tsw:actb1_takru IN IN FI actb1_takru.antigenic FP /^##sequence-region ACTB1_TAKRU 1 375\n/ FP /^#!Type Protein\n/ FP /^ACTB1_TAKRU\tantigenic\tepitope\t214\t222\t1\.207\t\+\t\.\tID=ACTB1_TAKRU\.1;note=\*pos 218\n/ FC = 23 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID backtranambig-ex AP backtranambig IN tsw:opsd_human IN FI opsd_human.fasta FP /^>OPSD_HUMAN/ FP /^ATGAAYGGNACNGARGGNCCNAAYTTYTAYGTNCCNTTYWSNAAYGCNACNGGNGTNGTN\n/ FP /^MGNWSNCCNTTYGARTAYCCNCARTAYTAYYTNGCNGARCCNTGGCARTTYWSNATGYTN\n/ FP /^TGGGTNATGGCNYTNGCNTGYGCNGCNCCNCCNYTNGCNGGNTGGWSNMGNTAYATHCCN\n/ FP /^GARACNWSNCARGTNGCNCCNGCN\n/ FZ = 1101 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID backtranseq-ex UC Note that this is a human protein and so the default human codon frequency file is used ie. is not specified AP backtranseq IN tsw:opsd_human IN FI opsd_human.fasta FP /^>OPSD_HUMAN/ FP /CGCCACCGGCGTGGTG\n/ FZ = 1101 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID backtranseq-ex2 UC This uses a drosophila sequence and codon table. AP backtranseq CL -cfile Edrome.cut IN tsw:ach2_drome IN FI ach2_drome.fasta FP /^>ACH2_DROME/ FP /GAGAAGAAGAAC\n/ FZ = 1832 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID backtranseq-nbrf UC Using an NBRF format sequence AP backtranseq IN ../../data/104k.nbrf IN FI 104k_thean.fasta FP /^>104K_THEAN/ FP /^GGCATCCTGTGA\n/ FZ = 2709 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID banana-data AP banana CL -outfile banana.data -nograph IN tembl:u68037 FI banana.data FC = 1219 FP /c 17\.7 20\.0\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID banana-ex AP banana CL -nooutfile -graph ps IN tembl:u68037 FI stdout FC = 1 FP /^Created banana\.ps\n/ FI banana.ps FC > 1 FP /%%Title: PLplot Graph\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID banana-ex2 AP banana CL -graph data IN tembl:u68037 FI banana.profile FZ = 25601 FP /^a +0\.0 +0\.0\nt +19\.7 +0\.0\ng +17\.7 +0\.0\na +21\.1 +0\.0\n/ FP /^a +14\.9 +0\.0\nc +17\.7 +20\.0\nc +15\.7 +19\.2\nt +15\.7 +18\.5\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 9 FP /^Created banana1\.dat\n/ FI banana1.dat FC > 1 FP /^##/ FI banana2.dat FC > 1 FP /^##/ FI banana3.dat FC > 1 FP /^##/ FI banana4.dat FC > 1 FP /^##/ FI banana5.dat FC > 1 FP /^##/ FI banana6.dat FC > 1 FP /^##/ FI banana7.dat FC > 1 FP /^##/ FI banana8.dat FC > 1 FP /^##/ FI banana9.dat FC > 1 FP /^##/ // ID biosed-ex UC Replace all 'T's with 'U's to create an RNA sequence AP biosed CL tembl:x65923 x65923.rna -target T -replace U FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.rna FZ = 563 FP /^UCUAAUAAAAAAGCCACUUAGUUCAGUCAAAAAAAAAA\n/ // ID biosed-ex2 UC Replace all 'PPP' protein motifs with 'XXPPPXX' AP biosed CL tsw:amir_pseae amir_pseae.pep -target PPP -replace XXPPPXX FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir_pseae.pep FZ = 251 FP /^MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWXXPPPXXESFDVPVDVV\n/ // ID btwisted-ex AP btwisted CL -auto tembl:ab000095 -sbegin 100 -send 120 FI ab000095.btwisted FP /^# Twisting calculated from 100 to 120 of AB000095\n/ FP /^Total twist \(degrees\): 681\.1\n/ FP /^Total turns : 1\.89\n/ FP /^Average bases per turn: 11\.10\n/ FP /^Total stacking energy : -179\.34\n/ FP /^Average stacking energy per dinucleotide: -8\.97\n/ // ID cai-ex AP cai CL TEMBL:AB009602 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ab009602.cai FP /0\.188/ // ID chaos-ex AP chaos CL tembl:j01636 -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI chaos.ps FZ > 100 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 17 FP /^Created chaos\.ps\n/ // ID chaos-data AP chaos CL tembl:j01636 -graph data FI stdout FC = 1 FP /^Created chaos1\.dat\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI chaos1.dat FC = 7495 FP /^##Maintitle Chaos game representation of tembl-id:J01636\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^##Screen x1 -0\.100000 y1 -0\.100000 x2 1\.400000 y2 1\.100000\n/ FP /^Line x1 0\.090456 y1 0\.242971 x2 0\.090556 y2 0\.242971 colour 0\n/ FP /^Text3 x1 0\.000000 y1 0\.000000 colour 0 size 1\.000000 A\n/ FP /^Text1 x1 1\.100000 y1 0\.750000 colour 0 size 0\.500000 A 1739\n/ FP /^Text1 x1 1\.100000 y1 0\.450000 colour 0 size 0\.500000 [%]A 23\.26\n/ // ID charge-ex AP charge CL tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hbb_human.charge FP /CHARGE of HBB_HUMAN from 1 to 147: window 5/ FC = 146 // ID checktrans-ex AP checktrans IN ../../data/paamir.pep IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI paamir_1.checktrans FZ = 132 FP /Total STOPS:\s+7\n/ FP /^\s+7\s+635\s+357\s+278-634\s+PAAMIR_1_7\n/ FI paamir_1.fasta FZ = 375 FP /\A>PAAMIR_1_7\n/ FP /^PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR\n/ FI paamir_1.gff FC = 6 FP /^PAAMIR_1\t\S+\t\S+\t278\t634\t\./ // ID chips-ex AP chips CL -sbeg 135 -send 1292 IN tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.chips FP /Nc = 32\.951/ // ID cirdna-ex AP cirdna CL -graph cps IN ../../data/data.cirp IN IN IN IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI cirdna.ps FC = 658 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 18 FP /^Created cirdna\.ps\n/ // ID codcmp-ex UC This compares the codon usage tables for Escherichia coli and Haemophilus influenzae. AP codcmp IN Eecoli.cut IN Ehaein.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.codcmp FP /^Mean Squared Difference = 0\.034\n/ FP /^Sum Squared Difference = 2\.178\n/ FP /^Root Mean Squared Difference = 0\.184\n/ FP /^Sum Difference = 9\.504\n/ FP /^Mean Difference = 0\.14[89]\n/ FP /^Codons not appearing = 0\n/ // ID codcopy-ex AP codcopy IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-outemboss AP codcopy DL keep CL -oformat emboss IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.emboss FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-outcut AP codcopy DL keep CL -oformat cut IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-outgcg AP codcopy DL keep CL -oformat gcg IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.gcg FC = 83 FP 64 /^[A-Z][a-z][a-z] +[ACGT][ACGT][ACGT]/ FP /^Asp GAC 30454\.00 19\.05 0\.37\n/ FP /^Asp GAT 51514\.00 32\.22 0\.63\n/ FP /^Ile ATC 39971\.00 25\.00 0\.42\n/ FP /^Leu CTG 84455\.00 52\.82 0\.50\n/ FP /^Met ATG 44414\.00 27\.78 1\.00\n/ FP /^End TAG 365\.00 0\.23 0\.07\n/ // ID codcopy-outcutg AP codcopy DL keep CL -oformat cutg IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cutg FC = 28 FP 16 /^[ACGU][ACGU][ACGU]/ FP /^Escherichia coli K12 \[gbbct\]: 5045 CDS's \(1598893 codons\)\n/ FP /^UUG 13\.7\( 21948\) UCG 8\.9\( 14256\) UAG 0\.2\( 365\) UGG 15\.3\( 24468\)\n/ FP /^CUG 52\.8\( 84455\) CCG 23\.2\( 37150\) CAG 28\.8\( 46100\) CGG 5\.4\( 8619\)\n/ FP /^AUC 25\.0\( 39971\) ACC 23\.4\( 37354\) AAC 21\.6\( 34554\) AGC 16\.0\( 25632\)\n/ FP /^AUG 27\.8\( 44414\) ACG 14\.4\( 22977\) AAG 10\.2\( 16305\) AGG 1\.2\( 1944\)\n/ FP /^GUU 18\.4\( 29410\) GCU 15\.4\( 24549\) GAU 32\.2\( 51514\) GGU 24\.8\( 39714\)\n/ FP /^GUC 15\.2\( 24336\) GCC 25\.5\( 40761\) GAC 19\.0\( 30454\) GGC 29\.4\( 47013\)\n/ FP /^Coding GC 51\.81% 1st letter GC 58\.93% 2nd letter GC 40\.69% 3rd letter GC 55\.80%\n/ // ID codcopy-outcutgaa AP codcopy DL keep CL -oformat cutgaa IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cutgaa FC = 29 FP 16 /^[ACGU][ACGU][ACGU]/ FP /^Escherichia coli K12 \[gbbct\]: 5045 CDS's \(1598893 codons\)\n/ FP /^UUG L 0\.13 13\.7 \( 21948\) UCG S 0\.15 8\.9 \( 14256\) UAG \* 0\.07 0\.2 \( 365\) UGG W 1\.00 15\.3 \( 24468\)\n/ FP /^CUG L 0\.50 52\.8 \( 84455\) CCG P 0\.52 23\.2 \( 37150\) CAG Q 0\.65 28\.8 \( 46100\) CGG R 0\.10 5\.4 \( 8619\)\n/ FP /^AUC I 0\.42 25\.0 \( 39971\) ACC T 0\.4[34] 23\.4 \( 37354\) AAC N 0\.55 21\.6 \( 34554\) AGC S 0\.28 16\.0 \( 25632\)\n/ FP /^AUG M 1\.00 27\.8 \( 44414\) ACG T 0\.27 14\.4 \( 22977\) AAG K 0\.23 10\.2 \( 16305\) AGG R 0\.02 1\.2 \( 1944\)\n/ FP /^GUU V 0\.26 18\.4 \( 29410\) GCU A 0\.16 15\.4 \( 24549\) GAU D 0\.63 32\.2 \( 51514\) GGU G 0\.34 24\.8 \( 39714\)\n/ FP /^GUC V 0\.2[12] 15\.2 \( 24336\) GCC A 0\.27 25\.5 \( 40761\) GAC D 0\.37 19\.0 \( 30454\) GGC G 0\.40 29\.4 \( 47013\)\n/ FP /^Coding GC 51\.81% 1st letter GC 58\.93% 2nd letter GC 40\.69% 3rd letter GC 55\.80%\n/ // ID codcopy-outspsum AP codcopy DL keep CL -oformat spsum IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.spsum FC = 2 FP 1 /^(\d+\s+){63}\d+\n/ FP /^Escherichia coli K12: 5045\n/ FP /^.* 84455 .* 30454 51514 .* 39971 .* 44414 .* 365 .*\n/ // ID codcopy-outcherry AP codcopy DL keep CL -oformat cherry IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cherry FC = 86 FP 64 /^[A-Z][a-z][a-z]\s+[ACGT][ACGT][ACGT]/ FP /^Escherichia coli K12\n/ FP /^5045 genes found in CUTG146\n/ FP /^Asp GAT 51514\.00 32\.22 0\.63\n/ FP /^Asp GAC 30454\.00 19\.05 0\.37\n/ FP /^Ile ATC 39971\.00 25\.00 0\.42\n/ FP /^Leu CTG 84455\.00 52\.82 0\.50\n/ FP /^Met ATG 44414\.00 27\.78 1\.00\n/ FP /^End TAG 365\.00 0\.23 0\.07\n/ // ID codcopy-outtransterm AP codcopy DL keep CL -oformat transterm IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.transterm FC = 83 FP 64 /^[A-Z][a-z][a-z]\s+[ACGT][ACGT][ACGT]/ FP /^Asp GAT 51514\.00 32\.22 0\.63\n/ FP /^Asp GAC 30454\.00 19\.05 0\.37\n/ FP /^Met ATG 44414\.00 27\.78 1\.00\n/ FP /^Ile ATC 39971\.00 25\.00 0\.42\n/ FP /^End TAG 365\.00 0\.23 0\.07\n/ FP /^Leu CTG 84455\.00 52\.82 0\.50\n/ // ID codcopy-outcodehop AP codcopy DL keep CL -oformat codehop IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.codehop FC = 68 FP 64 /^0\.[0-9]+\t-- \[[ 0-9][0-9]\] [ACGU][ACGU][ACGU]\n/ FP /^0\.024999\t-- \[13\] AUC\n/ FP /^0\.027778\t-- \[14\] AUG\n/ FP /^0\.052821\t-- \[30\] CUG\n/ FP /^0\.019047\t-- \[33\] GAC\n/ FP /^0\.032219\t-- \[35\] GAU\n/ FP /^0\.000228\t-- \[50\] UAG\n/ FP /^Eecoli\.cut\n/ FP /^Codon usage for Escherichia coli K12: 5045\n/ FP /^ from CUTG146\/gbbct: 1598893 codons\n/ // ID codcopy-outstaden AP codcopy DL keep CL -oformat staden IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.staden FC = 21 FP 16 /^\s+[A-Z] [ACGT][ACGT][ACGT]/ FP /^ L TTG 21948 S TCG 14256 \* TAG 365 W TGG 24468\n/ FP /^ L CTG 84455 P CCG 37150 Q CAG 46100 R CGG 8619\n/ FP /^ I ATC 39971 T ACC 37354 N AAC 34554 S AGC 25632\n/ FP /^ M ATG 44414 T ACG 22977 K AAG 16305 R AGG 1944\n/ FP /^ V GTT 29410 A GCT 24549 D GAT 51514 G GGT 39714\n/ FP /^ V GTC 24336 A GCC 40761 D GAC 30454 G GGC 47013\n/ // ID codcopy-outnumstaden AP codcopy DL keep CL -oformat numstaden IN Eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.numstaden FC = 21 FP 16 /^\s+[A-Z] [ACGT][ACGT][ACGT]/ FP /^ L TTG 21948 S TCG 14256 \* TAG 365 W TGG 24468\n/ FP /^ L CTG 84455 P CCG 37150 Q CAG 46100 R CGG 8619\n/ FP /^ I ATC 39971 T ACC 37354 N AAC 34554 S AGC 25632\n/ FP /^ M ATG 44414 T ACG 22977 K AAG 16305 R AGG 1944\n/ FP /^ V GTT 29410 A GCT 24549 D GAT 51514 G GGT 39714\n/ FP /^ V GTC 24336 A GCC 40761 D GAC 30454 G GGC 47013\n/ // ID codcopy-emboss AP codcopy CL -format emboss IN ../codcopy-outemboss/eecoli.emboss IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-cut AP codcopy CL -format cut IN ../codcopy-outcut/eecoli.cut IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-gcg AP codcopy CL -format gcg IN ../codcopy-outgcg/eecoli.gcg IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 72 FP 64 /^[ACGT][ACGT][ACGT]/ FP 0 /Escherichia/ FP 0 /gbbct/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.370 19\.050 30454\n/ FP /^GAT D 0\.630 32\.220 51514\n/ FP /^ATC I 0\.420 25\.000 39971\n/ FP /^CTG L 0\.500 52\.820 84455\n/ FP /^ATG M 1\.000 27\.780 44414\n/ FP /^TAG \* 0\.070 0\.230 365\n/ // ID codcopy-cutg AP codcopy CL -format cutg IN ../codcopy-outcutg/eecoli.cutg IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 74 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.000 30454\n/ FP /^GAT D 0\.628 32\.200 51514\n/ FP /^ATC I 0\.419 25\.000 39971\n/ FP /^CTG L 0\.496 52\.800 84455\n/ FP /^ATG M 1\.000 27\.800 44414\n/ FP /^TAG \* 0\.072 0\.200 365\n/ // ID codcopy-cutgaa AP codcopy CL -format cutgaa IN ../codcopy-outcutgaa/eecoli.cutgaa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 74 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.370 19\.000 30454\n/ FP /^GAT D 0\.630 32\.200 51514\n/ FP /^ATC I 0\.420 25\.000 39971\n/ FP /^CTG L 0\.500 52\.800 84455\n/ FP /^ATG M 1\.000 27\.800 44414\n/ FP /^TAG \* 0\.070 0\.200 365\n/ // ID codcopy-spsum AP codcopy CL -format spsum IN ../codcopy-outspsum/eecoli.spsum IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 73 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP 0 /gbbct/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-cherry AP codcopy CL -format cherry IN ../codcopy-outcherry/eecoli.cherry IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 74 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP 0 /gbbct/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.370 19\.050 30454\n/ FP /^GAT D 0\.630 32\.220 51514\n/ FP /^ATC I 0\.420 25\.000 39971\n/ FP /^CTG L 0\.500 52\.820 84455\n/ FP /^ATG M 1\.000 27\.780 44414\n/ FP /^TAG \* 0\.070 0\.230 365\n/ // ID codcopy-transterm AP codcopy CL -format transterm IN ../codcopy-outtransterm/eecoli.transterm IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 72 FP 64 /^[ACGT][ACGT][ACGT]/ FP 0 /Escherichia/ FP 0 /gbbct/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.370 19\.050 30454\n/ FP /^GAT D 0\.630 32\.220 51514\n/ FP /^ATC I 0\.420 25\.000 39971\n/ FP /^CTG L 0\.500 52\.820 84455\n/ FP /^ATG M 1\.000 27\.780 44414\n/ FP /^TAG \* 0\.070 0\.230 365\n/ // ID codcopy-codehop AP codcopy CL -format codehop IN ../codcopy-outcodehop/eecoli.codehop IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 75 FP 64 /^[ACGT][ACGT][ACGT]/ FP /^#Species: Escherichia coli K12\n/ FP /^#Division: gbbct\n/ FP /^#Release: CUTG146\n/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39970\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 364\n/ // ID codcopy-staden AP codcopy CL -format staden IN ../codcopy-outstaden/eecoli.staden IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 72 FP 64 /^[ACGT][ACGT][ACGT]/ FP 0 /Escherichia/ FP 0 /gbbct/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID codcopy-numstaden AP codcopy CL -format numstaden IN ../codcopy-outnumstaden/eecoli.numstaden IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eecoli.cut FC = 72 FP 64 /^[ACGT][ACGT][ACGT]/ FP 0 /Escherichia/ FP 0 /gbbct/ FP 0 /CUTG146/ FP /^#CdsCount: 5045\n/ FP /^#Coding GC 51\.81%\n/ FP /^#1st letter GC 58\.93%\n/ FP /^#2nd letter GC 40\.69%\n/ FP /^#3rd letter GC 55\.80%\n/ FP /^GAC D 0\.372 19\.047 30454\n/ FP /^GAT D 0\.628 32\.219 51514\n/ FP /^ATC I 0\.419 24\.999 39971\n/ FP /^CTG L 0\.496 52\.821 84455\n/ FP /^ATG M 1\.000 27\.778 44414\n/ FP /^TAG \* 0\.072 0\.228 365\n/ // ID coderet-ex UC To extract all of the CDS, mRNA, non-coding and the protein translations: AP coderet IN tembl:x03487 IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x03487.cds FP /^>x03487_cds_1\natgacgaccgcgt/ FI x03487.mrna FP /^>x03487_mrna_1\ncagacgttcttcgccgagagtcgtcggggttt/ FI x03487.prot FP /^>x03487_pro_1\nMTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMS/ FI x03487.noncoding FP /^>x03487_noncoding_501\ngtgagcgcgggc/ FI x03487.coderet FC = 3 FP / 1 1 6 1 8 X03487\n/ // ID coderet-ex2 UC To only extract the mRNA sequence: AP coderet CL -nocds -notranslation -norest IN tembl:X03487 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x03487.mrna FP /^>x03487_mrna_1\ncagacgttcttcgccgagagtcgtcggggttt/ FI x03487.coderet FC = 3 FP / 1 1 X03487\n/ // ID compseq-ex UC To count the frequencies of dinucleotides in a file: AP compseq CL tembl:x65923 -word 2 result3.comp FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result3.comp FZ = 913 FP /^Total count\s+517\n/ FP /^AA\s+45\s+0\.0870406\s+0\.0625000\s+1\.3926499\n/ // ID compseq-ex2 UC To count the frequencies of hexanucleotides, without outputting the results of hexanucleotides that do not occur in the sequence: AP compseq CL tembl:x65923 -word 6 result6.comp -nozero FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result6.comp FZ = 18690 FP /^Total count\s+513\n/ FP /^AAAAAA\s+6\s+0\.0116959\s+0\.0002441\s+47\.9064327\n/ // ID compseq-ex3 UC To count the frequencies of trinucleotides in frame 2 of a sequence and use a previously prepared compseq output to show the expected frequencies: AP compseq CL tembl:x65923 -word 3 result3.comp -frame 2 -in ../../data/prev.comp FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result3.comp FZ = 2698 FP /^Total count\s+172\n/ FP /^AAA\s+7\s+0\.0406977\s+0\.0329457\s+1\.2352955\n/ // ID cons-ex AP cons IN ../../data/dna.msf IN aligned.cons FI stderr FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FC = 2 FI aligned.cons FZ = 134 FP /\A>EMBOSS_001\n/ FP 2 /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID consambig-ex AP consambig IN ../../data/dna.msf IN aligned.consambig FI stderr FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FC = 2 FI aligned.consambig FZ = 134 FP /\A>EMBOSS_001\n/ FP /^ACGTACGTACGTACGTACGTacgtACGTACGTACGTACGTMSKWMSKWMSKWMSKWMSKW\n/ FP /^MSKWMSKWMSKWMSKWMSKWACGTACGTACGTACGTACGTACGTACGTWSSWACGTACGT\n/ // ID cpgplot-ex AP cpgplot CL tembl:u68037 -graph cps IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created cpgplot\.ps\n/ FI u68037.cpgplot FP /U68037 from 1 to 1218/ FP /Observed\/Expected ratio > 0\.60/ FP /Length 406 \(104\.\.509\)/ FP /Length 329 \(596\.\.924\)/ FI u68037.gff FP /^#!Type DNA\n/ FP /^##sequence-region U68037 1 924\n/ FI cpgplot.ps FP /^%%Title: PLplot Graph/ // ID cpgplot-old AP cpgplot CL tembl:u68037 -graph data IN IN IN IN IN IN FI stdout FC = 3 FP /^Created cpgplot3\.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI u68037.cpgplot FP /U68037 from 1 to 1218/ FP /Observed\/Expected ratio > 0\.60/ FP /Length 406 \(104\.\.509\)/ FP /Length 329 \(596\.\.924\)/ FI u68037.gff FC = 7 FP /^U68037\t\S+\t\S+\t104\t509\t/ FP /^U68037\t\S+\t\S+\t596\t924\t/ FI cpgplot1.dat FZ = 24865 FP /^444\.000000\s+1\.066856\n/ FI cpgplot2.dat FZ = 25979 FP /^444\.000000\s+75\.000000\n/ FI cpgplot3.dat FZ = 24863 FP /^444\.000000\s+1\.000000\n/ // ID cpgreport-ex AP cpgreport CL tembl:u68037 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI u68037.cpgreport FP /CPGREPORT of U68037 from 1 to 1218/ FP /U68037 12 13 17 1 100\.0 -/ FP /U68037 1183 1193 26 2 72\.7 2\.00/ FI u68037.gff FC = 11 FP /^U68037\tcpgreport\tsequence_feature\t96\t1032\t630\.000\t/ // ID cusp-ex UC This example uses only one input sequence. UC The normal use would be to use a set of coding sequences as the input. AP cusp CL -sbeg 135 -send 1292 IN tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.cusp FP /GCA +A +0\.077 +7\.772 +3/ FP /GCC +A +0\.462 +46\.632 +18/ FP /GCG +A +0\.462 +46\.632 +18/ FP /GCT +A +0\.000 +0\.000 +0/ // ID cutgextract-keep AP cutgextract DL keep PP mkdir CODONS PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI CODONS FI outfile.cutgextract FC = 9 FP 9 /^Writing .*\.cut/ // ID cutgextract-species AP cutgextract DL keep PP mkdir CODONS PP EMBOSS_DATA=./ PP export EMBOSS_DATA CL -species "Aedes *" IN ../../data IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI CODONS FI outfile.cutgextract FC = 3 FP 3 /^Writing .*\.cut/ // ID cutgextract-outfile AP cutgextract DL keep PP mkdir CODONS PP EMBOSS_DATA=./ PP export EMBOSS_DATA CL -species "Aedes *" -filename EAedes IN ../../data IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI CODONS FI outfile.cutgextract FC = 1 FP 1 /^Writing EAedes\.cut/ // ID cutseq-ex UC To remove bases 10 to 12 from a database entry and write to the new sequence file 'gatta2.seq': AP cutseq CL tembl:x13776 gatta2.seq -from=10 -to=12 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI gatta2.seq FZ = 2293 FP /^ggtaccgctcgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgatcta\n/ // ID cutseq-ex2 UC To remove the first 20 bases from 'tembl:x13776' and write it to 'jsh.seq': AP cutseq CL tembl:x13776 -from=1 -to=20 -out=jsh.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI jsh.seq FZ = 2275 FP /^tgctcgatcaccaccagccgggcgacgggaactgcacgatctacctggcgagcctggagc\n/ // ID cutseq-ex3 UC If the default start and end positions are accepted, then all of the sequence is removed! AP cutseq CL tembl:x13776 starta.seq -sbeg=-1000 -send=1290 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI starta.seq FZ = 92 FP /\A>X13776 X13776\.1 .* regulation\Z/ // ID dan-ex AP dan IN tembl:x13776 IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.dan FC = 2167 FP / +1 +20 +[+] +64\.9 +70\.0 .* ggtaccgctggccgagcatc *\n/ FP / +2 +21 +[+] +63\.7 +65\.0 .* gtaccgctggccgagcatct *\n/ // ID dan-ex2 UC An example of producing a plot of Tm: AP dan CL -plot -graph cps IN tembl:x13776 IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 15 FP /^Created dan\.ps\n/ FI dan.ps FP /^%%Title: PLplot Graph/ // ID dan-old UC An example of producing a plot of Tm: AP dan CL -plot -graph data IN tembl:x13776 IN IN IN IN IN FI stdout FC = 1 FP /^Created dan1\.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dan1.dat FZ = 46589 FP /^11\.000000\s+64\.921204\n/ FP /^2158\.000000\s+62\.373310\n/ // ID density-ex AP density CL tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.density FC = 2095 FP / +1 +1 +[+] +0\.000 0\.180 0\.330 0\.330 0\.160 0\.340 0\.660\n/ // ID density-ex2 AP density CL tembl:x13776 -display quad -graph cps FI stdout FC = 1 FP /^Created density\.ps\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI density.ps FP /^%%Title: PLplot Graph/ // ID density-ex3 AP density CL tembl:x13776 -display dual -graph cps FI stdout FC = 1 FP /^Created density\.ps\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI density.ps FP /^%%Title: PLplot Graph/ // ############################################# # Direct access database(s) ############################################# ID direct-all AP seqret CL "temblall:*" test.out -auto FI test.out FP 49 /^>/ // ID direct-filename AP seqret CL "temblvrt:*" test.out -auto FI test.out FP 31 /^>/ // ID direct-exclude AP seqret CL "temblrest:*" test.out -auto FI test.out FP 18 /^>/ // ############################################# # The qapblast database(s) ############################################# ID dbiblast-allsys-keep DL keep AP dbiblast CL -fields "acc,sv,des" IN swnew IN ../../data IN IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000swnew\.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI des.hit FZ = 576 FP s /\A.{300}\006/ FI des.trg FZ = 1839 FP s /\A.{308}1\000/ FI seqvn.hit FZ = 300 FP s /\A.{300}$/ FI seqvn.trg FZ = 300 FP s /\A.{300}$/ FI outfile.dbiblast FC = 39 FP 1 /^filename: / FP /# Fields: 4\n/ FP /# Files: 1\n/ FP /# File 1: .*\/data[\/\\]swnew\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Index sv: maxlen 0 items 0\n/ FP /Index des: maxlen 19 items 57\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-allnosys-keep DL keep AP dbiblast CL -fields "acc,sv,des" -nosystemsort IN swnew IN ../../data IN IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI des.hit FZ = 576 FP s /\A.{300}\006/ FI des.trg FZ = 1839 FP s /\A.{308}1\000/ FI seqvn.hit FZ = 300 FP s /\A.{300}$/ FI seqvn.trg FZ = 300 FP s /\A.{300}$/ FI outfile.dbiblast FC = 40 FP 1 /^filename: / FP /# Fields: 4\n/ FP /# Files: 1\n/ FP /# File 1: .*\/data[\/\\]swnew\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Index sv: maxlen 0 items 0\n/ FP /Index des: maxlen 19 items 57\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-nosys-keep DL keep AP dbiblast CL -nosystemsort IN swnew IN ../../data IN IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI outfile.dbiblast FC = 33 FP 1 /^filename: / FP /# Fields: 2\n/ FP /# Files: 1\n/ FP /# File 1: .*\/data[\/\\]swnew\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-ex-keep UC This creates EMBOSS indices for the BLAST database 'swnew' DL keep AP dbiblast IN swnew IN ../../data IN IN IN IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000swnew.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI outfile.dbiblast FC = 32 FP 1 /^filename: / FP /# Fields: 2\n/ FP /# Files: 1\n/ FP /# File 1: .*\/data[\/\\]swnew\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-idfirst AP seqret CL qapblast-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiblast-idsecond AP seqret CL qapblast-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbiblast-last AP seqret CL qapblast-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbiblast-nextlast AP seqret CL qapblast-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbiblast-acfirst AP seqret CL qapblast-acc:P53450 test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU P53450 / FP 1 /^>/ // ID dbiblast-acsecond AP seqret CL qapblast-acc:P79755 test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU P79755 / FP 1 /^>/ // ID dbiblast-aclast AP seqret CL qapblast-acc:Q90515 test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU Q90515 / FP 1 /^>/ // ID dbiblast-all AP seqret CL "qapblast:*" test.out -auto FI test.out FZ = 4474 FP 1 /^>TM21_FUGRU Q90515 / FP 9 /^>/ // ID dbiblast-wild AP seqret CL "qapblast:n*" test.out -auto FI test.out FZ = 516 FP 2 /^>N/ FP 2 /^>/ // ############################################# # The qapblastsplit database(s) ############################################# ID dbiblast-split-keep DL keep AP dbiblast IN swsplit IN ../../data IN swsplit.*.pin IN IN IN P IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 410 FP s /\A.{300}\001\000swsplit\.00\.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI outfile.dbiblast FC = 50 FP 5 /^filename: / FP /# Fields: 2\n/ FP /# Files: 5\n/ FP /# File 1: .*\/data[\/\\]swsplit\.00\.pin\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Total 5 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-split-wild-keep DL keep AP dbiblast IN swsplit IN ../../data IN swsplit.*.* IN IN IN P IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 410 FP s /\A.{300}\001\000swsplit\.00\.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI outfile.dbiblast FC = 60 FP 5 /^filename: / FP /# Fields: 2\n/ FP /# Files: 15\n/ FP /# File \d+: .*\/data[\/\\]swsplit\.00\.pin\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Total 5 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-split-list-keep DL keep AP dbiblast IN swsplit IN ../../data IN swsplit.00.pin swsplit.01.pin swsplit.02.pin swsplit.03.pin swsplit.04.pin IN IN IN P IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 410 FP s /\A.{300}\001\000swsplit\.00\.pin\000/ FI entrynam.idx FZ = 480 FP s /\A.{300}CO9_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\006/ FI acnum.trg FZ = 426 FP s /\A.{308}O42493\001/ FI outfile.dbiblast FC = 50 FP 5 /^filename: / FP /# Fields: 2\n/ FP /# Files: 5\n/ FP /# File \d+: .*\/data[\/\\]swsplit\.00\.pin\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Total 5 files 9 entries \(0 duplicates\)\n/ // ID dbiblast-split-idfirst AP seqret CL qapblastsplit-id:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiblast-split-idsecond AP seqret CL qapblastsplit-id:E2BB_FUGRU test.out -auto FI test.out FZ = 473 FP 1 /^>E2BB_FUGRU / FP 1 /^>/ // ID dbiblast-split-last AP seqret CL qapblastsplit-id:TM21_FUGRU test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU / FP 1 /^>/ // ID dbiblast-split-nextlast AP seqret CL qapblastsplit-id:ODO2_FUGRU test.out -auto FI test.out FZ = 569 FP 1 /^>ODO2_FUGRU / FP 1 /^>/ // ID dbiblast-split-acfirst AP seqret CL qapblastsplit-acc:P53450 test.out -auto FI test.out FZ = 435 FP 1 /^>FOS_FUGRU P53450 / FP 1 /^>/ // ID dbiblast-split-acsecond AP seqret CL qapblastsplit-acc:P79755 test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU P79755 / FP 1 /^>/ // ID dbiblast-split-aclast AP seqret CL qapblastsplit-acc:Q90515 test.out -auto FI test.out FZ = 287 FP 1 /^>TM21_FUGRU Q90515 / FP 1 /^>/ // ID dbiblast-split-all AP seqret CL "qapblastsplit:*" test.out -auto FI test.out FZ = 4474 FP 1 /^>TM21_FUGRU Q90515 / FP 9 /^>/ // ID dbiblast-split-wild AP seqret CL "qapblastsplit:n*" test.out -auto FI test.out FZ = 516 FP 2 /^>N/ FP 2 /^>/ // ID dbiblast-split-testexc AP seqret CL qapblastsplitexc:CO9_FUGRU test.out -auto FI test.out FZ = 649 FP 1 /^>CO9_FUGRU / FP 1 /^>/ // ID dbiblast-split-testexcall AP seqret CL "qapblastsplitexc:*" test.out -auto FI test.out FZ = 3864 FP 1 /^>CO9_FUGRU / FP 7 /^>/ // ID dbiblast-split-testexcfail ER 1 AP seqret CL qapblastsplitexc:FABP_FUGRU test.out -auto FI stderr FZ = 131 FP /Error: Unable to read sequence 'qapblastsplitexc:FABP_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbiblast-split-testinc AP seqret CL qapblastsplitinc:FABP_FUGRU test.out -auto FI test.out FZ = 175 FP 1 /^>FABP_FUGRU / FP 1 /^>/ // ID dbiblast-split-testincall AP seqret CL "qapblastsplitinc:*" test.out -auto FI test.out FZ = 610 FP 1 /^>FABP_FUGRU / FP 2 /^>/ // ID dbiblast-split-testincfail ER 1 AP seqret CL qapblastsplitinc:CO9_FUGRU test.out -auto FI stderr FZ = 130 FP /Error: Unable to read sequence 'qapblastsplitinc:CO9_FUGRU'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qanfasta database ############################################# ID dbifasta-ex-keep DL keep AP dbifasta IN EMROD IN idacc IN ../../data IN emrod IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp binary FZ = 322 FP s /\A.{300}\001\000emrod\000/ FI entrynam.idx binary FZ = 396 FP s /\A.{300}L48662\000/ FI acnum.hit binary FZ = 324 FP s /\A.{300}\001/ FI acnum.trg binary FZ = 384 FP s /\A.{308}L48662\001/ FI outfile.dbifasta FC = 34 FP /^# Fields: 2\n/ FP /^# Field 2: acc\n/ FP /^# File 1: \S+\/data[\/\\]emrod\n/ FP /^filename: 'emrod'\n/ FP 1 /^filename: / FP /^ id: 6\n/ FP /^ acc: 6\n/ FP /^Index acc: maxlen 6 items 6\n/ FP /^Total 1 files 6 entries \(0 duplicates\)\n/ // ID dbifasta-allsys-keep DL keep AP dbifasta CL -fields "acc,sv,des" IN EMROD IN idacc IN ../../data IN emrod IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000emrod\000/ FI entrynam.idx FZ = 396 FP s /\A.{300}L48662\000/ FI acnum.hit FZ = 324 FP s /\A.{300}\001/ FI acnum.trg FZ = 384 FP s /\A.{308}L48662\001/ FI seqvn.hit FZ = 300 FP s /\A.{44} +/ FI seqvn.trg FZ = 300 FP s /\A.{44} +/ FI des.hit FZ = 580 FP s /\A.{300}\001/ FP s /\A.{44} +/ FI des.trg FZ = 1140 FP s /\A.{308}1\000/ FP s /\A.{44} +/ FI outfile.dbifasta FC = 41 FP /^# Fields: 4\n/ FP /^# Field 2: acc\n/ FP /^# File 1: \S+\/data[\/\\]emrod\n/ FP /^filename: 'emrod'\n/ FP 1 /^filename: / FP /^ id: 6\n/ FP /^ acc: 6\n/ FP /^ sv: 0\n/ FP /^ des: 71\n/ FP /^Index acc: maxlen 6 items 6\n/ FP /^Index sv: maxlen 0 items 0\n/ FP /^Index des: maxlen 13 items 40\n/ FP /^Total 1 files 6 entries \(0 duplicates\)\n/ // ID dbifasta-allnosys-keep DL keep AP dbifasta CL -fields "acc,sv,des" -nosystemsort IN EMROD IN idacc IN ../../data IN emrod IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp binary FZ = 322 FP s /\A.{300}\001\000emrod\000/ FI entrynam.idx binary FZ = 396 FP s /\A.{300}L48662\000/ FI acnum.hit binary FZ = 324 FP s /\A.{300}\001/ FI acnum.trg binary FZ = 384 FP s /\A.{308}L48662\001/ FI seqvn.hit binary FZ = 300 FP s /\A.{44} +/ FI seqvn.trg binary FZ = 300 FP s /\A.{44} +/ FI des.hit binary FZ = 580 FP s /\A.{300}\001/ FP s /\A.{44} +/ FI des.trg binary FZ = 1140 FP s /\A.{308}1\000/ FP s /\A.{44} +/ FI outfile.dbifasta FC = 42 FP /^# Fields: 4\n/ FP /^# Field 2: acc\n/ FP /^# File 1: \S+\/data[\/\\]emrod\n/ FP /^filename: 'emrod'\n/ FP 1 /^filename: / FP /^ id: 6\n/ FP /^ acc: 6\n/ FP /^ sv: 0\n/ FP /^ des: 71\n/ FP /^Index acc: maxlen 6 items 6\n/ FP /^Index sv: maxlen 0 items 0\n/ FP /^Index des: maxlen 13 items 40\n/ FP /^Total 1 files 6 entries \(0 duplicates\)\n/ // ID dbifasta-idfirst AP seqret CL qanfasta-id:L48662 test.out -auto FI test.out FZ = 475 FP 1 /^>L48662 / FP 1 /^>/ // ID dbifasta-idsecond AP seqret CL qanfasta-id:M11903 test.out -auto FI test.out FZ = 861 FP 1 /^>M11903 / FP 1 /^>/ // ID dbifasta-last AP seqret CL qanfasta-id:Z46957 test.out -auto FI test.out FZ = 1568 FP 1 /^>Z46957 / FP 1 /^>/ // ID dbifasta-nextlast AP seqret CL qanfasta-id:U68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>U68037 / FP 1 /^>/ // ID dbifasta-all AP seqret CL "qanfasta:*" test.out -auto FI test.out FZ = 5586 FP 1 /^>U68037 / FP 6 /^>/ // ID dbifasta-wild AP seqret CL "qanfasta:m*" test.out -auto FI test.out FZ = 2225 FP 1 /^>M11903 / FP 3 /^>M1190/ FP 3 /^>/ // ############################################# # The qapfasta database ############################################# ID dbifasta-swiss-keep DL keep AP dbifasta IN SWNEW IN idacc IN ../../data IN swnew IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000swnew\000/ FI entrynam.idx FZ = 498 FP s /\A.{300}O42495_FUGRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\001/ FI acnum.trg FZ = 426 FP s /\A.{308}O42495\001/ FI outfile.dbifasta FC = 34 FP /# Fields: 2\n/ FP /# Files: 1\n/ FP /# File 1: \S+\/data[\/\\]swnew\n/ FP 1 /^filename: / FP /Index acc: maxlen 6 items 9\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ // ID dbifasta-swiss-idfirst AP seqret CL qapfasta-id:O42495_FUGRU test.out -auto FI test.out FZ = 470 FP 1 /^>O42495_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-idsecond AP seqret CL qapfasta-id:Q1KKT3_FUGRU test.out -auto FI test.out FZ = 465 FP 1 /^>Q1KKT3_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-last AP seqret CL qapfasta-id:Q68HA9_FUGRU test.out -auto FI test.out FZ = 678 FP 1 /^>Q68HA9_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-nextlast AP seqret CL qapfasta-id:Q50J40_FUGRU test.out -auto FI test.out FZ = 440 FP 1 /^>Q50J40_FUGRU / FP 1 /^>/ // ID dbifasta-swiss-all AP seqret CL "qapfasta:*" test.out -auto FI test.out FZ = 4654 FP 1 /^>Q2KT90_FUGRU / FP 9 /^>/ // ID dbifasta-swiss-wild AP seqret CL "qapfasta:q2*" test.out -auto FI test.out FZ = 960 FP 1 /^>Q2KT90_FUGRU / FP 3 /^>Q2/ FP 3 /^>/ // ############################################# # The qawfasta database ############################################# ID dbifasta-worm-keep DL keep AP dbifasta IN WORM IN simple IN ../../data IN wormpep.clone.* IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 344 FP s /\A.{300}\001\000wormpep\.clone\.AB\000/ FI entrynam.idx FZ = 1488 FP s /\A.{300}AC3\.1\000/ FI acnum.hit FZ = 564 FP s /\A.{300}\001/ FI acnum.trg FZ = 1356 ## Pattern needs 's' modifier ... binary data includes a newline FP s /\A.{308}AC3\.1\000/ FI outfile.dbifasta FC = 38 FP /# Fields: 2\n/ FP /# Files: 2\n/ FP 2 /^filename: / FP /Index acc: maxlen 8 items 66\n/ FP /Total 2 files 66 entries \(0 duplicates\)\n/ // ID dbifasta-worm-idfirst AP seqret CL qawfasta-id:AC3.1 test.out -auto FI test.out FZ = 426 FP 1 /^>AC3\.1 / FP 1 /^>/ // ID dbifasta-worm-idsecond AP seqret CL qawfasta-id:AC3.2 test.out -auto FI test.out FZ = 1057 FP 1 /^>AC3\.2 / FP 1 /^>/ // ID dbifasta-worm-last AP seqret CL qawfasta-id:ZK637.15 test.out -auto FI test.out FZ = 205 FP 1 /^>ZK637\.15 / FP 1 /^>/ // ID dbifasta-worm-nextlast AP seqret CL qawfasta-id:zk637.14 test.out -auto FI test.out FZ = 260 FP 1 /^>ZK637\.14 / FP 1 /^>/ // ID dbifasta-worm-all AP seqret CL "qawfasta:*" test.out -auto FI test.out FZ = 33816 FP 66 /^>/ // ID dbifasta-worm-wild AP seqret CL "qawfasta:a*" test.out -auto FI test.out FZ = 19764 FP 40 /^>A[^\n]+\n[^>]/ FP 40 /^>/ // ID dbifasta-worm-wildz AP seqret CL "qawfasta:z*" test.out -auto FI test.out FZ = 7264 FP 15 /^>Z[^\n]+\n[^>]/ FP 15 /^>/ // ############################################# # The qanflat database ############################################# ID dbiflat-ex-keep DL keep AP dbiflat IN EMBL IN EMBL IN ../../embl IN rod.dat IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000rod\.dat\000/ FI entrynam.idx FZ = 396 FP s /\A.{300}L48662\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\001/ FI acnum.trg FZ = 398 FP s /\A.{308}L48662\001/ FI outfile.dbiflat FC = 34 FP /# Release: 0\.0\n/ FP /# Date: [0-9][0-9]\/[0-9][0-9]\/[0-9][0-9]\n/ FP /# Files: 1\n/ FP /# File 1: .*[\/\\]rod\.dat\n/ FP /# Fields: 2\n/ FP /# Rundate: [A-Z][a-z][a-z] \d+ [A-Z][a-z][a-z] 20[0-9][0-9] 12:00:00\n/ FP 1 /^Index \S+ maxlen \d+ items \d+\n/ FP 1 /^filename: / // ID dbiflat-nosys-keep DL keep AP dbiflat CL -nosystemsort IN EMBL IN EMBL IN ../../embl IN rod.dat IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000rod\.dat\000/ FI entrynam.idx FZ = 396 FP s /\A.{300}L48662\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\001/ FI acnum.trg FZ = 398 FP s /\A.{308}L48662\001/ FI outfile.dbiflat FC = 35 FP /# Release: 0\.0\n/ FP /# Date: \d\d\/\d\d\/[0-9][0-9]\n/ FP /# Files: 1\n/ FP /# File 1: .*[\/\\]rod\.dat\n/ FP /# Fields: 2\n/ FP /# Rundate: [A-Z][a-z][a-z] \d\d [A-Z][a-z][a-z] 20[0-9][0-9] 12:00:00\n/ FP 1 /^Index \S+ maxlen \d+ items \d+\n/ FP 1 /^filename: / // ID dbiflat-id AP seqret CL qanflat-id:M11905 test.out -auto FI test.out FZ = 654 FP /\A>M11905 / FP 1 /^>/ // ID dbiflat-idfirst AP seqret CL qanflat-id:L48662 test.out -auto FI test.out FZ = 475 FP 1 /^>L48662 / FP 1 /^>/ // ID dbiflat-idsecond AP seqret CL qanflat-id:M11903 test.out -auto FI test.out FZ = 861 FP 1 /^>M11903 / FP 1 /^>/ // ID dbiflat-last AP seqret CL qanflat-id:Z46957 test.out -auto FI test.out FZ = 1568 FP 1 /^>Z46957 / FP 1 /^>/ // ID dbiflat-nextlast AP seqret CL qanflat-id:U68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>U68037 / FP 1 /^>/ // ID dbiflat-all AP seqret CL "qanflat:*" test.out -auto FI test.out FZ = 5586 FP 1 /^>L48662 / FP 6 /^>/ // ID dbiflat-wild AP seqret CL "qanflat:*7" test.out -auto FI test.out FZ = 2886 FP 1 /^>Z46957 / FP 2 /^>/ // ID dbiflat-wild2 AP seqret CL "qanflat:m119*" test.out -auto FI test.out FZ = 2225 FP 1 /^>M11904 / FP 3 /^>/ // ID dbiflat-tembl-idfirst AP seqret CL tembl-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbiflat-tembl-idsecond AP seqret CL tembl-id:AB000360 test.out -auto FI test.out FZ = 2685 FP 1 /^>AB000360 / FP 1 /^>/ // ID dbiflat-tembl-last AP seqret CL tembl-id:Z69719 test.out -auto FI test.out FZ = 34396 FP 1 /^>Z69719 / FP 1 /^>/ // ID dbiflat-tembl-nextlast AP seqret CL tembl-id:Z52466 test.out -auto FI test.out FZ = 500 FP 1 /^>Z52466 / FP 1 /^>/ // ID dbiflat-tembl-multiacc AP seqret CL tembl-acc:X01958 test.out -auto FI test.out FZ = 2225 FP 3 /^>M1190/ FP 3 /^>/ // ID dbiflat-tembl-all AP seqret CL "tembl:*" test.out -auto FI test.out FZ = 2837964 FP 3 /^>AF/ FP 3 /^>M1190/ FP 49 /^>/ // ID dbiflat-tembl-wild AP seqret CL "tembl:a*" test.out -auto FI test.out FZ = 322239 FP 3 /^>AF/ FP 9 /^>/ // ID dbiflat-tembl-keyspace AP seqret CL "tembl-key:lacy gene" test.out -osformat embl -auto FI test.out FZ = 27203 FP 2 /^KW .*; lacY gene;/ FP 2 /^ID / // ID dbiflat-tembl-keywild AP seqret CL "tembl-key:a*" test.out -auto FI test.out FZ = 90158 FP 1 />U01317 / FP 7 />/ // ############################################# # The qapflat database ############################################# ID dbiflat-swiss-keep DL keep AP dbiflat IN SWNEW IN IN ../../swnew IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000trembl\.dat\000/ FI entrynam.idx FZ = 498 FP s /\A.{300}O42495_TAKRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\001/ FI acnum.trg FZ = 426 FP s /\A.{308}O42495\001/ FI outfile.dbiflat FC = 32 FP /# Fields: 2\n/ FP /# Files: 1\n/ FP /# Filenames: \*\.dat\n/ FP /filename: 'trembl\.dat'\n id: 9\n/ FP /Index acc: maxlen 6 items 9\n/ FP /^Total 1 files 9 entries \(0 duplicates\)\n/ FP 1 /^Index \S+ maxlen \d+ items \d+\n/ FP 1 /^filename: / // ID dbiflat-swiss-allsys-keep DL keep AP dbiflat CL -fields "acc,sv,des,key,org" IN SWNEW IN IN ../../swnew IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000trembl\.dat\000/ FI entrynam.idx FZ = 498 FP s /\A.{300}O42495_TAKRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\001/ FI acnum.trg FZ = 426 FP s /\A.{308}O42495\001/ FI des.trg FZ = 1402 FP s /\A.{308}1\000/ FI des.hit FZ = 536 FP s /\A.{300}\004/ FI keyword.trg FZ = 1020 FP s /\A.{308}COPPER\000/ FI keyword.hit FZ = 412 FP s /\A.{300}\006/ FI seqvn.trg FZ = 444 FP s /\A.{308}O42495\.0\001/ FI seqvn.hit FZ = 336 FP s /\A.{300}\001/ FI taxon.trg FP s /\A.{308}ACANTHOMORPHA\000/ FZ = 867 FI taxon.hit FZ = 1056 FP s /\A.{300}\001/ FI outfile.dbiflat FC = 45 FP /# Fields: 6\n/ FP /# Field 6: org\n/ FP /# Files: 1\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Index sv: maxlen 8 items 9\n/ FP /Index des: maxlen 21 items 38\n/ FP /Index key: maxlen 28 items 20\n/ FP /Index org: maxlen 19 items 21\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ FP 5 /^Index \S+ maxlen \d+ items \d+\n/ FP 1 /^filename: / // ID dbiflat-swiss-allnosys-keep DL keep AP dbiflat CL -nosystemsort -fields "acc,sv,des,key,org" IN SWNEW IN IN ../../swnew IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 322 FP s /\A.{300}\001\000trembl\.dat\000/ FI entrynam.idx FZ = 498 FP s /\A.{300}O42495_TAKRU\000/ FI acnum.hit FZ = 336 FP s /\A.{300}\001/ FI acnum.trg FZ = 426 FP s /\A.{308}O42495\001/ FI des.trg FZ = 1402 FP s /\A.{308}1\000/ FI des.hit FZ = 536 FP s /\A.{300}\004/ FI keyword.trg FZ = 1020 FP s /\A.{308}COPPER\000/ FI keyword.hit FZ = 412 FP s /\A.{300}\006/ FI seqvn.trg FZ = 444 FP s /\A.{308}O42495\.0\001/ FI seqvn.hit FZ = 336 FP s /\A.{300}\001/ FI taxon.trg FP s /\A.{308}ACANTHOMORPHA\000/ FZ = 867 FI taxon.hit FZ = 1056 FP s /\A.{300}\001/ FI outfile.dbiflat FC = 46 FP /# Fields: 6\n/ FP /# Field 6: org\n/ FP /# Files: 1\n/ FP /Index acc: maxlen 6 items 9\n/ FP /Index sv: maxlen 8 items 9\n/ FP /Index des: maxlen 21 items 38\n/ FP /Index key: maxlen 28 items 20\n/ FP /Index org: maxlen 19 items 21\n/ FP /Total 1 files 9 entries \(0 duplicates\)\n/ FP 5 /^Index \S+ maxlen \d+ items \d+\n/ FP 1 /^filename: / // ID dbiflat-swiss-idfirst AP seqret CL qapflat-id:O42495_TAKRU test.out -auto FI test.out FZ = 471 FP 1 /^>O42495_TAKRU / FP 1 /^>/ // ID dbiflat-swiss-idsecond AP seqret CL qapflat-id:Q1KKT3_TAKRU test.out -auto FI test.out FZ = 466 FP 1 /^>Q1KKT3_TAKRU / FP 1 /^>/ // ID dbiflat-swiss-last AP seqret CL qapflat-id:Q68HA9_TAKRU test.out -auto FI test.out FZ = 679 FP 1 /^>Q68HA9_TAKRU / FP 1 /^>/ // ID dbiflat-swiss-nextlast AP seqret CL qapflat-id:Q50J40_TAKRU test.out -auto FI test.out FZ = 441 FP 1 /^>Q50J40_TAKRU / FP 1 /^>/ // ID dbiflat-swiss-all AP seqret CL "qapflat:*" test.out -auto FI test.out FZ = 4657 FP 1 /^>Q2KT90_TAKRU / FP 9 /^>/ // ID dbiflat-swiss-wild AP seqret CL "qapflat:q2*" test.out -auto FI test.out FZ = 957 FP 1 /^>Q2KT90_TAKRU / FP 3 /^>/ // ID dbiflat-embl-allsys-keep DL keep AP dbiflat CL -fields "acc,sv,des,key,org" IN EMBL IN IN ../../embl IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 520 ## We need the s modifier ## because there is a linefeed in the header binary stuff FP s /\A.{300}\001\000est\.dat\000/ FI entrynam.idx FZ = 1182 FP s /\A.{300}AB000095Y/ FI acnum.hit FZ = 916 FP s /\A.{300}\001/ FI acnum.trg FZ = 2732 ## We need the s modifier ## because there is a linefeed in the header binary stuff FP s /\A.{308}AB000095\001/ FI des.trg FZ = 6132 FP s /\A.{308}1\000/ FI des.hit FZ = 2080 FP s /\A.{300}\006/ FI keyword.trg FZ = 4356 FP s /\A.{308}ACETYLTRANSFERASE\000/ FI keyword.hit FZ = 668 FP s /\A.{300}\015/ FI seqvn.trg FZ = 1182 FP s /\A.{308}AB000095\.1\001/ FI seqvn.hit FZ = 496 FP s /\A.{300}\001/ FI taxon.trg FP s /\A.{308}AFRICAN CLAWED FROG\000/ FZ = 5025 FI taxon.hit FZ = 3016 FP s /\A.{300}\017/ FI outfile.dbiflat FC = 117 FP /# Fields: 6\n/ FP /# Field 6: org\n/ FP /# Files: 10\n/ FP /Index acc: maxlen 8 items 152\n/ FP /Index sv: maxlen 10 items 49\n/ FP /Index des: maxlen 19 items 216\n/ FP /Index key: maxlen 44 items 78\n/ FP /Index org: maxlen 27 items 135\n/ FP /Total 10 files 49 entries \(0 duplicates\)\n/ FP 5 /^Index \S+ maxlen \d+ items \d+\n/ FP 10 /^filename: / // ID dbiflat-embl-allnosys-keep DL keep AP dbiflat CL -nosystemsort -fields "acc,sv,des,key,org" IN EMBL IN IN ../../embl IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 520 ## We need the s modifier ## because there is a linefeed in the header binary stuff FP s /\A.{300}\001\000est\.dat\000/ FI entrynam.idx FZ = 1182 FP s /\A.{300}AB000095Y/ FI acnum.hit FZ = 916 FP s /\A.{300}\001/ FI acnum.trg FZ = 2732 ## We need the s modifier ## because there is a linefeed in the header binary stuff FP s /\A.{308}AB000095\001/ FI des.trg FZ = 6132 FP s /\A.{308}1\000/ FI des.hit FZ = 2080 FP s /\A.{300}\006/ FI keyword.trg FZ = 4356 FP s /\A.{308}ACETYLTRANSFERASE\000/ FI keyword.hit FZ = 668 FP s /\A.{300}\015/ FI seqvn.trg FZ = 1182 FP s /\A.{308}AB000095\.1\001/ FI seqvn.hit FZ = 496 FP s /\A.{300}\001/ FI taxon.trg FP s /\A.{308}AFRICAN CLAWED FROG\000/ FZ = 5025 FI taxon.hit FZ = 3016 FP s /\A.{300}\017/ FI outfile.dbiflat FC = 118 FP /# Fields: 6\n/ FP /# Field 6: org\n/ FP /# Files: 10\n/ FP /Index acc: maxlen 8 items 152\n/ FP /Index sv: maxlen 10 items 49\n/ FP /Index des: maxlen 19 items 216\n/ FP /Index key: maxlen 44 items 78\n/ FP /Index org: maxlen 27 items 135\n/ FP /Total 10 files 49 entries \(0 duplicates\)\n/ FP 5 /^Index \S+ maxlen \d+ items \d+\n/ FP 10 /^filename: / // ID dbiflat-embl-testexc AP seqret CL qanflatexc-id:X13776 test.out -auto FI test.out FZ = 2296 FP 1 /^>X13776 / FP 1 /^>/ // ID dbiflat-embl-testexcall AP seqret CL "qanflatexc-id:*" test.out -auto FI test.out FZ = 2832378 FP 1 /^>X13776 / FP 43 /^>/ // ID dbiflat-embl-testexcfail ER 1 AP seqret CL qanflatexc-id:U68037 test.out -auto FI stderr FZ = 124 FP /Error: Unable to read sequence 'qanflatexc-id:U68037'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbiflat-embl-testinc AP seqret CL qanflatinc-id:U68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>U68037 / FP 1 /^>/ // ID dbiflat-embl-testincall AP seqret CL "qanflatinc-id:*" test.out -auto FI test.out FZ = 5586 FP 1 /^>U68037 / FP 6 /^>/ // ID dbiflat-embl-testincfail ER 1 AP seqret CL qanflatinc-id:X13776 test.out -auto FI stderr FZ = 124 FP /Error: Unable to read sequence 'qanflatinc-id:X13776'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbiflat-genbank-keep DL keep AP dbiflat IN GENBANK IN GENBANK IN ../../genbank IN *.seq IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 520 ## Pattern needs 's' modifier ... binary data includes a newline FP s /\A.{300}\001\000gbbct1\.seq\000/ FI entrynam.idx FZ = 1041 FP s /\A.{300}AB000095\000/ FI acnum.hit FZ = 620 FP s /\A.{300}\001/ FI acnum.trg FZ = 1580 FP s /\A.{308}AB000095\001/ FI outfile.dbiflat FC = 70 FP /# Fields: 2\n/ FP /# Files: 10\n/ FP /filename: 'gbbct1\.seq'\n id: 9\n/ FP /filename: 'gbest1\.seq'\n id: 1\n/ FP /filename: 'gbinv1\.seq'\n id: 2\n/ FP /filename: 'gbpln1\.seq'\n id: 1\n/ FP /filename: 'gbpln2\.seq'\n id: 1\n/ FP /filename: 'gbpri1\.seq'\n id: 18\n/ FP /filename: 'gbrod1\.seq'\n id: 3\n/ FP /filename: 'gbsts1\.seq'\n id: 1\n/ FP /filename: 'gbvrl1\.seq'\n id: 1\n/ FP /filename: 'gbvrt\.seq'\n id: 2\n/ FP /Index acc: maxlen 8 items 80\n/ FP /Total 10 files 39 entries \(0 duplicates\)\n/ FP 1 /^Index \S+ maxlen \d+ items \d+\n/ FP 10 /^filename: / // ############################################# # The qangcg database(s) ############################################# ID dbigcg-ex-keep DL keep TI 120 AP dbigcg IN EMBL IN EMBL IN ../../embl IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 606 FP s /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/ FI entrynam.idx FZ = 1020 FP s /\A.{300}AB000095/ FI acnum.hit FZ = 492 FP s /\A.{300}\001/ FI acnum.trg FZ = 1068 FP s /\A.{308}AB000095/ FI outfile.dbigcg FC = 65 FP 9 /^filename: / FP /# Fields: 2\n/ FP /# Files: 9\n/ FP /# File \d+: .*\/embl[\/\\]eem_ba1\.seq\n/ FP /Index acc: maxlen 8 items 48\n/ FP /Total 9 files 40 entries \(0 duplicates\)\n/ // ID dbigcg-id AP seqret CL qangcg-id:X65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbigcg-idfirst AP seqret CL qangcg-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbigcg-idsecond AP seqret CL qangcg-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbigcg-last AP seqret CL qangcg-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbigcg-nextlast AP seqret CL qangcg-id:Z69719 test.out -auto FI test.out FZ = 34577 FP 1 /^>Z69719 / FP 1 /^>/ // ID dbigcg-acc AP seqret CL qangcg:L07770 test.out -auto FI test.out FZ = 1775 FP 1 /^>L07770 / FP 1 /^>/ // ID dbigcg-splitfirst AP seqret CL qangcg-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbigcg-splitmid AP seqret CL qangcg-id:AL034557 test.out -auto FI test.out FZ = 399267 FP 1 /^>AL034557 / FP 1 /^>/ // ID dbigcg-splitbefore AP seqret CL qangcg-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbigcg-splitafter AP seqret CL qangcg-id:AL035476 test.out -auto FI test.out FZ = 326444 FP 1 /^>AL035476 / FP 1 /^>/ // ID dbigcg-splitend AP seqret CL qangcg-id:U18997 test.out -auto FI test.out FZ = 378731 FP 1 /^>U18997 / FP 1 /^>/ // ID dbigcg-all AP seqret CL "qangcg:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>L07770 / FP 40 /^>/ // ID dbigcg-wild AP seqret CL "qangcg:a*" test.out -auto FI test.out FZ = 1251303 FP 3 /^>AB/ FP 9 /^>A/ FP 9 /^>/ // ID dbigcg-testexc AP seqret CL qangcgexc-id:x65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbigcg-testexcall AP seqret CL "qangcgexc-id:*" test.out -auto FI test.out FZ = 1744803 FP 1 /^>X65923 / FP 30 /^>/ // ID dbigcg-testexcfail ER 1 AP seqret CL qangcgexc-id:j01636 test.out -auto FI stderr FZ = 123 FP /Error: Unable to read sequence 'qangcgexc-id:j01636'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbigcg-testinc AP seqret CL qangcginc-id:j01636 test.out -auto FI test.out FZ = 7677 FP 1 /\A>J01636 / FP 1 /^>/ // ID dbigcg-testincall AP seqret CL "qangcginc-id:*" test.out -auto FI test.out FZ = 400271 FP 1 /^>J01636 / FP 10 /^>/ // ID dbigcg-testincfail ER 1 AP seqret CL qangcginc-id:x65923 test.out -auto FI stderr FZ = 123 FP /Error: Unable to read sequence 'qangcginc-id:x65923'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qangcgall database(s) ############################################# ID dbigcg-allsys-keep DL keep TI 120 AP dbigcg CL -fields "acc,sv,des,key,org" IN EMBL IN EMBL IN ../../embl IN IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 606 FP s /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/ FI entrynam.idx FZ = 1020 FP s /\A.{300}AB000095/ FI acnum.hit FZ = 492 FP s /\A.{300}\001/ FI acnum.trg FZ = 1068 FP s /\A.{308}AB000095/ FI des.hit FZ = 1824 FP s /\A.{300}\023/ FI des.trg FZ = 5754 FP s /\A.{308}0\000/ FI keyword.hit FZ = 588 FP s /\A.{300}\047/ FI keyword.trg FZ = 3264 FP s /\A.{308}16P13\000/ FI seqvn.hit FZ = 396 FP s /\A.{300}\001/ FI seqvn.trg FZ = 732 FP s /\A.{308}AB000095\.1/ FI taxon.hit FZ = 2036 FP s /\A.{300}\016/ FI taxon.trg FZ = 3765 FP s /\A.{308}AFRICAN CLAWED FROG\000/ FI outfile.dbigcg FC = 110 FP 9 /^filename: / FP /# Fields: 6\n/ FP /# Files: 9\n/ FP /# File \d+: .*\/embl[\/\\]eem_ba1\.seq\n/ FP /Index acc: maxlen 8 items 48\n/ FP /Index sv: maxlen 10 items 24\n/ FP /Index des: maxlen 19 items 202\n/ FP /Index key: maxlen 44 items 57\n/ FP /Index org: maxlen 27 items 99\n/ FP /Total 9 files 40 entries \(0 duplicates\)\n/ // ID dbigcg-allsys-id AP seqret CL qangcgall-id:x65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbigcg-allsys-idfirst AP seqret CL qangcgall-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbigcg-allsys-idsecond AP seqret CL qangcgall-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbigcg-allsys-last AP seqret CL qangcgall-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbigcg-allsys-nextlast AP seqret CL qangcgall-id:Z69719 test.out -auto FI test.out FZ = 34577 FP 1 /^>Z69719 / FP 1 /^>/ // ID dbigcg-allsys-acc AP seqret CL qangcgall:L07770 test.out -auto FI test.out FZ = 1775 FP 1 /^>L07770 / FP 1 /^>/ // ID dbigcg-allsys-splitfirst AP seqret CL qangcgall-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbigcg-allsys-splitmid AP seqret CL qangcgall-id:AL034557 test.out -auto FI test.out FZ = 399267 FP 1 /^>AL034557 / FP 1 /^>/ // ID dbigcg-allsys-splitbefore AP seqret CL qangcgall-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbigcg-allsys-splitafter AP seqret CL qangcgall-id:AL035476 test.out -auto FI test.out FZ = 326444 FP 1 /^>AL035476 / FP 1 /^>/ // ID dbigcg-allsys-splitend AP seqret CL qangcgall-id:U18997 test.out -auto FI test.out FZ = 378731 FP 1 /^>U18997 / FP 1 /^>/ // ID dbigcg-allsys-all AP seqret CL "qangcgall:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbigcg-allsys-wild AP seqret CL "qangcgall:a*" test.out -auto FI test.out FZ = 1251303 FP 9 /^>A/ FP 3 /^>AB/ FP 9 /^>/ // ID dbigcg-allsys-acnum AP seqret CL qangcgall-acc:X65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbigcg-allsys-acnumall AP seqret CL "qangcgall-acc:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbigcg-allsys-acnumwild AP seqret CL "qangcgall-acc:x*" test.out -auto FI test.out FZ = 18988 FP 11 /^>[A-Z0-9]+ X/ FP 11 /^>/ // ID dbigcg-allsys-sv AP seqret CL qangcgall-sv:D00596.1 test.out -auto FI test.out FZ = 19008 FP 1 /^>D00596 / FP 1 /^>/ // ID dbigcg-allsys-svall AP seqret CL "qangcgall-sv:*" test.out -auto FI test.out FZ = 2066925 FP 0 /^>X65923 / FP 1 /^>D00596 / FP 24 /^>/ // ID dbigcg-allsys-svwild AP seqret CL "qangcgall-sv:x*" test.out -auto FI test.out FZ = 5043 FP 3 /^>X/ FP 3 /^>/ // ID dbigcg-allsys-des AP seqret CL qangcgall-des:fau test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbigcg-allsys-desall AP seqret CL "qangcgall-des:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbigcg-allsys-deswild AP seqret CL "qangcgall-des:m*" test.out -auto FI test.out FZ = 1543931 FP 18 /^>.* [Mm]/ FP 18 /^>/ // ID dbigcg-allsys-key AP seqret CL qangcgall-key:rhodopsin test.out -auto FI test.out FZ = 5086 FP 1 /^>L07770 / FP 3 /^>/ // ID dbigcg-allsys-keyall AP seqret CL "qangcgall-key:*" test.out -auto FI test.out FZ = 1470428 FP 1 /^>L07770 / FP 35 /^>/ // ID dbigcg-allsys-keyspace AP seqret CL "qangcgall-key:lacy gene" test.out -osformat embl -auto FI test.out FZ = 26226 FP 2 /^KW .*; lacY gene;/ FP 2 /^ID / // ID dbigcg-allsys-org AP seqret CL qangcgall-org:Mus test.out -auto FI test.out FZ = 475 FP 1 /^>L48662 / FP 1 /^>/ // ID dbigcg-allsys-orgall AP seqret CL "qangcgall-org:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbigcg-allsys-orgwild AP seqret CL "qangcgall-org:s*" test.out -auto FI test.out FZ = 45442 FP 1 /^>L48662/ FP 5 /^>/ // ID dbigcg-allsys-orgwild2 AP seqret CL "qangcgall-org:mus*" test.out -auto FI test.out FZ = 4276 FP 1 /^>L48662/ FP 2 /^>/ // ID dbigcg-allnosys-keep DL keep TI 120 AP dbigcg CL -fields "acc,sv,des,key,org" -nosystem IN EMBL IN EMBL IN ../../embl IN IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 606 FP s /\A.{300}\001\000eem_ba1\.ref eem_ba1\.seq\000/ FI entrynam.idx FZ = 1020 FP s /\A.{300}AB000095/ FI acnum.hit FZ = 492 FP s /\A.{300}\001/ FI acnum.trg FZ = 1068 FP s /\A.{308}AB000095/ FI des.hit FZ = 1824 FP s /\A.{300}\023/ FI des.trg FZ = 5754 FP s /\A.{308}0\000/ FI keyword.hit FZ = 588 FP s /\A.{300}\047/ FI keyword.trg FZ = 3264 FP s /\A.{308}16P13\000/ FI seqvn.hit FZ = 396 FP s /\A.{300}\001/ FI seqvn.trg FZ = 732 FP s /\A.{308}AB000095\.1/ FI taxon.hit FZ = 2036 FP s /\A.{300}\016/ FI taxon.trg FZ = 3765 FP s /\A.{308}AFRICAN CLAWED FROG\000/ FI outfile.dbigcg FC = 111 FP 9 /^filename: / FP /# Fields: 6\n/ FP /# Files: 9\n/ FP /# File \d+: .*\/embl[\/\\]eem_ba1\.seq\n/ FP /Index acc: maxlen 8 items 48\n/ FP /Index sv: maxlen 10 items 24\n/ FP /Index des: maxlen 19 items 202\n/ FP /Index key: maxlen 44 items 57\n/ FP /Index org: maxlen 27 items 99\n/ FP /Total 9 files 40 entries \(0 duplicates\)\n/ // ############################################# # The qapir database(s) ############################################# ID dbigcg-pir-keep DL keep TI 120 AP dbigcg IN PIR IN PIR IN ../../pir IN IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 388 FP s /\A.{300}\001\000pir1\.ref pir1\.seq\000/ FI entrynam.idx FZ = 1260 FP s /\A.{300}A31558/ FI acnum.hit FZ = 672 FP s /\A.{300}\033/ FI acnum.trg FZ = 1392 FP s /\A.{308}A00001/ FI outfile.dbigcg FC = 45 FP 4 /^filename: / FP /# Fields: 2\n/ FP /# Files: 4\n/ FP /# File \d+: .*\/pir[\/\\]pir1\.seq\n/ FP /Index acc: maxlen 6 items 78\n/ FP /Total 4 files 60 entries \(0 duplicates\)\n/ // ID dbigcg-pir-id AP seqret CL qapir-id:cchu test.out -auto FI test.out FZ = 153 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbigcg-pir-idfirst AP seqret CL qapir-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbigcg-pir-idsecond AP seqret CL qapir-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbigcg-pir-last AP seqret CL qapir-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbigcg-pir-nextlast AP seqret CL qapir-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbigcg-pir-acc AP seqret CL qapir:A00001 test.out -auto FI test.out FZ = 153 FP 1 /^>CCHU / FP 1 /^>/ // ID dbigcg-pir-all AP seqret CL "qapir:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>S11172 / FP 60 /^>/ // ID dbigcg-pir-wild AP seqret CL "qapir:c*" test.out -auto FI test.out FZ = 7969 FP 49 /^>C/ FP 49 /^>/ // ID dbigcg-pir-testexc AP seqret CL qapirexc-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /\A>S11172 / FP 1 /^>/ // ID dbigcg-pir-testexcall AP seqret CL "qapirexc-id:*" test.out -auto FI test.out FZ = 2498 FP 1 /^>S11172 / FP 11 /^>/ // ID dbigcg-pir-testexcfail ER 1 AP seqret CL qapirexc-id:cchu test.out -auto FI stderr FZ = 120 FP /Error: Unable to read sequence 'qapirexc-id:cchu'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbigcg-pir-testinc AP seqret CL qapirinc-id:cchu test.out -auto FI test.out FZ = 153 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbigcg-pir-testincall AP seqret CL "qapirinc-id:*" test.out -auto FI test.out FZ = 7969 FP 1 /^>CCHU / FP 49 /^>/ // ID dbigcg-pir-testincfail ER 1 AP seqret CL qapirinc-id:S11172 test.out -auto FI stderr FZ = 122 FP /Error: Unable to read sequence 'qapirinc-id:S11172'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qapirall database(s) ############################################# # field sv not supported by PIR format data ID dbigcg-pirall-keep DL keep TI 120 AP dbigcg CL -fields "acc,des,key,org" IN PIR IN PIR IN ../../pir IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI division.lkp FZ = 388 FP s /\A.{300}\001\000pir1\.ref pir1\.seq\000/ FI entrynam.idx FZ = 1260 FP s /\A.{300}A31558/ FI acnum.hit FZ = 672 FP s /\A.{300}\033/ FI acnum.trg FZ = 1392 FP s /\A.{308}A00001/ FI des.hit FZ = 1576 FP s /\A.{300}\066/ FI des.trg FZ = 3292 FP s /\A.{308}0/ FI keyword.hit FZ = 2196 FP s /\A.{300}\005/ FI keyword.trg FZ = 828 FP s /\A.{308}ACETYLATED AMINO END/ FI taxon.hit FZ = 768 FP s /\A.{300}\$/ FI taxon.trg FZ = 4944 FP s /\A.{308}AILANTHUS SILKMOTH/ FP /\000ANAS PLATYRHYNCHOS\000/ FP /\000DOMESTIC DUCK\000/ FI outfile.dbigcg FC = 64 FP 4 /^filename: / FP /# Fields: 5\n/ FP /# Files: 4\n/ FP /# File \d+: .*\/pir[\/\\]pir1\.seq\n/ FP /Index acc: maxlen 6 items 78\n/ FP /Index des: maxlen 14 items 136\n/ FP /Index key: maxlen 25 items 16\n/ FP /Index org: maxlen 35 items 108\n/ FP /Total 4 files 60 entries \(0 duplicates\)\n/ // ID dbigcg-pirall-id AP seqret CL qapirall-id:cchu test.out -auto FI test.out FZ = 153 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbigcg-pirall-idfirst AP seqret CL qapirall-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbigcg-pirall-idsecond AP seqret CL qapirall-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbigcg-pirall-last AP seqret CL qapirall-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbigcg-pirall-nextlast AP seqret CL qapirall-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbigcg-pirall-acc AP seqret CL qapirall:A00001 test.out -auto FI test.out FZ = 153 FP 1 /^>CCHU / FP 1 /^>/ // ID dbigcg-pirall-all AP seqret CL "qapirall:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>S11172 / FP 60 /^>/ // ID dbigcg-pirall-wild AP seqret CL "qapirall:c*" test.out -auto FI test.out FZ = 7969 FP 49 /^>C/ FP 49 /^>/ // ID dbigcg-pirall-acnum AP seqret CL qapirall-acc:A04605 test.out -auto FI test.out FZ = 151 FP 1 /\A>CCRT / FP 1 /^>/ // ID dbigcg-pirall-acnumall AP seqret CL "qapirall-acc:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>CCRT / FP 60 /^>/ // ID dbigcg-pirall-acnumwild AP seqret CL "qapirall-acc:s*" test.out -auto FI test.out FZ = 841 ## CCHO has an S* secondary accession number, rest are primary FP 4 /^>[A-Z0-9]+ S/ FP 5 /^>/ // ID dbigcg-pirall-des AP seqret CL qapirall-des:cytochrome test.out -auto FI test.out FZ = 8825 FP 1 />CCHU / FP 54 /^>/ // ID dbigcg-pirall-desall AP seqret CL "qapirall-des:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>CCHU / FP 60 /^>/ // ID dbigcg-pirall-deswild AP seqret CL "qapirall-des:p*" test.out -auto FI test.out FZ = 2399 FP 11 /^>.*[ -][Pp]/ FP 11 /^>/ // ID dbigcg-pirall-key AP seqret CL qapirall-key:polymorphism test.out -auto FI test.out FZ = 153 FP 1 /^>CCHU / FP 1 /^>/ // ID dbigcg-pirall-keyall AP seqret CL "qapirall-key:*" test.out -auto FI test.out FZ = 9109 FP 1 /^>CCHU / FP 56 /^>/ // # only entries with keywords ID dbigcg-pirall-keyall2 AP seqret CL "qapirall-key:?*" test.out -auto FI test.out FZ = 9109 FP 1 /^>CCHU / FP 56 /^>/ // ID dbigcg-pirall-keyspace AP entret CL "qapirall-key:blocked amino end" test.out -auto FI test.out FZ = 11846 FP 1 /^>P1;CCRT/ FP 8 /^>/ FP 8 /^C;Keywords:.*blocked amino end;/ // ID dbigcg-pirall-keywild AP seqret CL "qapirall-key:m*" test.out -auto FI test.out FZ = 8825 FP 1 /^>CCHU / FP 54 /^>/ // ID dbigcg-pirall-org AP seqret CL "qapirall-org:drosophila melanogaster" test.out -auto FI test.out FZ = 180 FP 1 /^>CCFFDM / FP 1 /^>/ // ID dbigcg-pirall-orgall AP seqret CL "qapirall-org:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>CCHU / FP 60 /^>/ // ID dbigcg-pirall-orgwild AP seqret CL "qapirall-org:s*" test.out -auto FI test.out FZ = 2010 FP 1 /^>CCPG / FP 12 /^>/ // ID dbigcg-pirall-orgwild2 AP seqret CL "qapirall-org:mus*" test.out -auto FI test.out FZ = 324 FP 1 /^>CCMS / FP 2 /^>/ // ############################################# # The qanxfasta database ############################################# ID dbxfasta-ex-keep DL keep AP dbxfasta IN emrod IN emblresource IN idacc IN ../../data IN emrod IN IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxfasta FC = 3 FP /Processing file: emrod entries: 6 \(6\) / FP 1 /Processing file: / FI emrod.ent FC = 5 FP 1 /^# Number of files: 1\n/ FP /^emrod\n/ FI emrod.pxac FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 6\n/ FP 1 /^Fullcount 6\n/ FP 1 /^Kwlimit 15\n/ FI emrod.pxid FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 6\n/ FP 1 /^Fullcount 6\n/ FP 1 /^Kwlimit 15\n/ FI emrod.xac FZ = 2143 FP 1 /z46957/ FP 1 /u68037/ FI emrod.xid FZ = 2143 FP 1 /z46957/ FP 1 /u68037/ // ID dbxfasta-allsys-keep DL keep AP dbxfasta CL -fields "id,acc,sv,des" IN emrod IN emblresource IN idacc IN ../../data IN emrod IN IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxfasta FC = 3 FP /Processing file: emrod entries: 6 \(6\) / FP 1 /Processing file: / FI emrod.ent FC = 5 FP 1 /^# Number of files: 1\n/ FP /^emrod\n/ FI emrod.pxac FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 6\n/ FP 1 /^Fullcount 6\n/ FP 1 /^Kwlimit 15\n/ FI emrod.pxde FZ = 181 FP 1 /^Type Secondary\n/ FP 1 /^Pages 123\n/ FP 1 /^Order 60\n/ FP 1 /^Fill 41\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 40\n/ FP 1 /^Fullcount 70\n/ FP 1 /^Kwlimit 20\n/ FI emrod.pxid FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 6\n/ FP 1 /^Fullcount 6\n/ FP 1 /^Kwlimit 15\n/ FI emrod.pxsv FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Pages 1\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 0\n/ FP 1 /^Kwlimit 15\n/ FI emrod.xac FZ = 2143 FP 1 /z46957/ FP 1 /u68037/ FI emrod.xde FZ = 8066 FP 1 /\000chromosome\000/ FP 2 /\000anti/ FI emrod.xid FZ = 2143 FP 1 /z46957/ FP 1 /u68037/ FI emrod.xsv FZ = 2048 FP 2047 /\000/ // ID dbxfasta-idfirst AP seqret CL qanxfasta-id:L48662 test.out -auto FI test.out FZ = 475 FP 1 /^>L48662 / FP 1 /^>/ // ID dbxfasta-idsecond AP seqret CL qanxfasta-id:M11903 test.out -auto FI test.out FZ = 861 FP 1 /^>M11903 / FP 1 /^>/ // ID dbxfasta-last AP seqret CL qanxfasta-id:Z46957 test.out -auto FI test.out FZ = 1568 FP 1 /^>Z46957 / FP 1 /^>/ // ID dbxfasta-nextlast AP seqret CL qanxfasta-id:U68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>U68037 / FP 1 /^>/ // ID dbxfasta-all AP seqret CL "qanxfasta:*" test.out -auto FI test.out FZ = 5586 FP 1 /^>U68037 / FP 3 /^>M1190/ FP 6 /^>/ // ID dbxfasta-wild AP seqret CL "qanxfasta:m*" test.out -auto FI test.out FZ = 2225 FP 1 /^>M11904 / FP 3 /^>M/ FP 3 /^>/ // ############################################# # The qapfasta database ############################################# ID dbxfasta-swiss-keep DL keep AP dbxfasta IN swnew IN swissresource IN idacc IN ../../data IN swnew IN IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxfasta FC = 3 FP /Processing file: swnew entries: 9 \(9\) / FP 1 /Processing file: / FI swnew.ent FC = 5 FP 1 /^# Number of files: 1\n/ FP /^swnew\n/ FI swnew.pxac FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 9\n/ FP 1 /^Fullcount 9\n/ FP 1 /^Kwlimit 15\n/ FI swnew.pxid FZ = 178 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 9\n/ FP 1 /^Fullcount 9\n/ FP 1 /^Kwlimit 15\n/ FI swnew.xac FZ = 2143 FP 2 /\000o42495\000/ FP 1 /\000q1kkt3\000/ FI swnew.xid FZ = 2149 FP 1 /\000q1kkt3_fugru\000/ // ID dbxfasta-swiss-idfirst AP seqret CL qapxfasta-id:O42495_FUGRU test.out -auto FI test.out FZ = 470 FP 1 /^>O42495_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-idsecond AP seqret CL qapxfasta-id:Q1KKT3_FUGRU test.out -auto FI test.out FZ = 465 FP 1 /^>Q1KKT3_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-last AP seqret CL qapxfasta-id:Q68HA9_FUGRU test.out -auto FI test.out FZ = 678 FP 1 /^>Q68HA9_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-nextlast AP seqret CL qapxfasta-id:Q50J40_FUGRU test.out -auto FI test.out FZ = 440 FP 1 /^>Q50J40_FUGRU / FP 1 /^>/ // ID dbxfasta-swiss-all AP seqret CL "qapxfasta:*" test.out -auto FI test.out FZ = 4654 FP 1 /^>Q2KT90_FUGRU / FP 9 /^>/ // ID dbxfasta-swiss-wild AP seqret CL "qapxfasta:q2*" test.out -auto FI test.out FZ = 960 FP 1 /^>Q2KT90_FUGRU / FP 3 /^>Q2/ FP 3 /^>/ // ############################################# # The qawfasta database ############################################# ID dbxfasta-worm-keep DL keep AP dbxfasta IN worm IN swissresource IN simple IN ../../data IN wormpep.clone.* IN IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxfasta FC = 4 FP 2 /Processing file: / FP 2 /Processing file: wormpep\.clone\./ FP 1 /Processing file: wormpep\.clone\.ZK637 entries: 66 \(15\) / FI worm.ent FC = 6 FP 1 /# Number of files: 2\n/ FP 1 /^wormpep\.clone\.AB\n/ FP 1 /^wormpep\.clone\.ZK637\n/ FI worm.pxac FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Pages 4\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 66\n/ FP 1 /^Fullcount 66\n/ FP 1 /^Kwlimit 15\n/ FI worm.pxid FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Pages 4\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 66\n/ FP 1 /^Fullcount 66\n/ FP 1 /^Kwlimit 15\n/ FI worm.xid FZ = 3691 FP 1 /\000ah10\.1\000/ FI worm.xac FZ = 3691 FP 1 /\000ah10\.1\000/ // ID dbxfasta-worm-idfirst AP seqret CL qawxfasta-id:AC3.1 test.out -auto FI test.out FZ = 426 FP 1 /^>AC3\.1 / FP 1 /^>/ // ID dbxfasta-worm-idsecond AP seqret CL qawxfasta-id:AC3.2 test.out -auto FI test.out FZ = 1057 FP 1 /^>AC3\.2 / FP 1 /^>/ // ID dbxfasta-worm-last AP seqret CL qawxfasta-id:ZK637.15 test.out -auto FI test.out FZ = 205 FP 1 /^>ZK637\.15 / FP 1 /^>/ // ID dbxfasta-worm-nextlast AP seqret CL qawxfasta-id:zk637.14 test.out -auto FI test.out FZ = 260 FP 1 /^>ZK637\.14 / FP 1 /^>/ // ID dbxfasta-worm-all AP seqret CL "qawxfasta:*" test.out -auto FI test.out FZ = 33816 FP 66 /^>/ // ID dbxfasta-worm-wild AP seqret CL "qawxfasta:a*" test.out -auto FI test.out FZ = 19764 FP 40 /^>A[^\n]+\n[^>]/ FP 40 /^>/ // ID dbxfasta-worm-wildz AP seqret CL "qawxfasta:z*" test.out -auto FI test.out FZ = 7264 FP 15 /^>Z[^\n]+\n[^>]/ FP 15 /^>/ // ############################################# # The qanxflat database ############################################# ID dbxflat-ex-keep DL keep AP dbxflat IN embl IN emblresource IN embl IN rod.dat IN ../../embl IN IN IN FI stderr FC = 13 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxflat FC = 3 FP /^Processing file: rod\.dat entries: 6 \(6\)/ FP 1 /^Processing file: / FI embl.ent FC = 5 FP /^# Number of files: 1\n/ FP /^rod\.dat\n/ FI embl.pxac FZ = 178 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 6\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 7\n/ FP /^Fullcount 9\n/ FP /^Kwlimit 15\n/ FI embl.pxid FZ = 178 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 3\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 6\n/ FP /^Fullcount 6\n/ FP /^Kwlimit 15\n/ FI embl.xac FZ = 2496 FP /\000l48662\000/ FP /\000l48662\000/ FP /\000z46957\000/ FP /\000u68037\000/ FI embl.xid FZ = 2143 FP /\000l48662\000/ FP /\000z46957\000/ FP /\000u68037\000/ // ID dbxflat-id AP seqret CL qanxflat-id:M11905 test.out -auto FI test.out FZ = 654 FP /\A>M11905 / FP 1 /^>/ // ID dbxflat-idfirst AP seqret CL qanxflat-id:L48662 test.out -auto FI test.out FZ = 475 FP 1 /^>L48662 / FP 1 /^>/ // ID dbxflat-idsecond AP seqret CL qanxflat-id:M11903 test.out -auto FI test.out FZ = 861 FP 1 /^>M11903 / FP 1 /^>/ // ID dbxflat-last AP seqret CL qanflat-id:Z46957 test.out -auto FI test.out FZ = 1568 FP 1 /^>Z46957 / FP 1 /^>/ // ID dbxflat-nextlast AP seqret CL qanxflat-id:U68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>U68037 / FP 1 /^>/ // ID dbxflat-all AP seqret CC Fails to fetch all entries in emboss access method CL "qanxflat:*" test.out -auto FI test.out FZ = 5586 FP 1 /^>L48662 / FP 6 /^>/ // ID dbxflat-wild AP seqret CL "qanxflat:*7" test.out -auto FI test.out FZ = 2886 FP 1 /^>Z46957 / FP 2 /^>/ // ID dbxflat-wild2 AP seqret CL "qanxflat:m119*" test.out -auto FI test.out FZ = 2225 FP 1 /^>M11904 / FP 3 /^>/ // ############################################# # The qanxflatall database ############################################# ID dbxflat-all-keep DL keep AP dbxflat CL -fields "id,acc,sv,des,key,org" IN embl IN emblresource IN embl IN IN ../../embl IN IN FI stderr FC = 7 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxflat FC = 12 FP /^Processing file: .*rod\.dat entries: 43 \(6\)/ FP 10 /^Processing file: / FI embl.ent FC = 14 FP /^# Number of files: 10\n/ FP /^rod\.dat\n/ FP 10 /^[a-z0-9]+\.dat\n/ FI embl.pxac FZ = 183 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 11\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 152\n/ FP /^Fullcount 154\n/ FP /^Kwlimit 15\n/ FI embl.pxde FZ = 183 FP /Type Secondary\n/ FP /^Compress Yes\n/ FP /^Pages 647\n/ FP /^Order 60\n/ FP /^Fill 41\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 71\n/ FP /^Fill2 101\n/ FP /^Count 213\n/ FP /^Fullcount 417\n/ FP /^Kwlimit 20\n/ FI embl.pxid FZ = 180 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 3\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 49\n/ FP /^Fullcount 49\n/ FP /^Kwlimit 15\n/ FI embl.pxkw FZ = 181 FP /Type Secondary\n/ FP /^Compress Yes\n/ FP /^Pages 241\n/ FP /^Order 31\n/ FP /^Fill 25\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 71\n/ FP /^Fill2 101\n/ FP /^Count 78\n/ FP /^Fullcount 92\n/ FP /^Kwlimit 50\n/ FI embl.pxsv FZ = 180 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 3\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 49\n/ FP /^Fullcount 49\n/ FP /^Kwlimit 15\n/ FI embl.pxtx FZ = 183 FP /Type Secondary\n/ FP /^Compress Yes\n/ FP /^Pages 413\n/ FP /^Order 46\n/ FP /^Fill 34\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 71\n/ FP /^Fill2 101\n/ FP /^Count 135\n/ FP /^Fullcount 679\n/ FP /^Kwlimit 30\n/ FI embl.xac FZ = 7888 FP /\000l48662\000/ FP /\000z46957\000/ FP /\000u68037\000/ FI embl.xde FZ = 34946 FP 2 /\000complement\000/ FI embl.xid FZ = 2548 FP /\000l48662\000/ FP /\000z46957\000/ FP /\000u68037\000/ FI embl.xkw FZ = 14116 FP 2 /\000beta_globin\000/ FI embl.xsv FZ = 2572 FP /\000h45989\.1\000/ FI embl.xtx FZ = 28449 FP 1 /\000homo_sapiens\000/ // ID dbxflatall-id AP seqret CL qanxflatall-id:L07770 test.out -auto FI test.out FZ = 1775 FP /\A>L07770 / FP 1 />/ // ID dbxflatall-idfirst AP seqret CL qanxflatall-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 />AB000095 / FP 1 />/ // ID dbxflatall-idsecond AP seqret CL qanxflatall-id:AB000360 test.out -auto FI test.out FZ = 2685 FP 1 />AB000360 / FP 1 />/ // ID dbxflatall-last AP seqret CL qanxflatall-id:Z69719 test.out -auto FI test.out FZ = 34396 FP 1 />Z69719 / FP 1 />/ // ID dbxflatall-nextlast AP seqret CL qanxflatall-id:Z52466 test.out -auto FI test.out FZ = 500 FP 1 />Z52466 / FP 1 />/ // ID dbxflatall-all AP seqret CC Fails to fetch all entries in emboss access method CL "qanxflatall:*" test.out -auto FI test.out FZ = 2837964 FP 1 />X13776 / FP 49 />/ // ID dbxflatall-wild AP seqret CL "qanxflatall:a*" test.out -auto FI test.out FZ = 322239 FP 3 />AF/ FP 9 />A/ FP 9 />/ // ID dbxflatall-multiacc AP seqret CL qanxflatall-acc:X01958 test.out -auto FI test.out FZ = 2225 FP 3 /^>M1190/ FP 3 /^>/ // ID dbxflatall-keyspace AP seqret CL "qanxflatall-key:lacy gene" test.out -osf embl -auto FI test.out FZ = 27203 FP 2 /^KW .*; lacY gene;/ FP 2 /^ID / // ID dbxflatall-keywild AP seqret CL "qanxflatall-key:a*" test.out -auto FI test.out FZ = 90158 FP 1 />U01317 / FP 7 />/ // ID dbxflat-embl-testexc AP seqret CL qanxflatexc-id:X13776 test.out -auto FI test.out FZ = 2296 FP 1 /^>X13776 / FP 1 /^>/ // ID dbxflat-embl-testexcall AP seqret CL "qanxflatexc-id:*" test.out -auto FI test.out FZ = 2832378 FP 1 /^>X13776 / FP 43 /^>/ // ID dbxflat-embl-testexcfail ER 1 AP seqret CL qanxflatexc-id:U68037 test.out -auto FI stderr FZ = 125 FP /Error: Unable to read sequence 'qanxflatexc-id:U68037'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbxflat-embl-testinc AP seqret CL qanxflatinc-id:U68037 test.out -auto FI test.out FZ = 1318 FP 1 /^>U68037 / FP 1 /^>/ // ID dbxflat-embl-testincall AP seqret CL "qanxflatinc-id:*" test.out -auto FI test.out FZ = 5586 FP 1 /^>U68037 / FP 6 /^>/ // ID dbxflat-embl-testincfail ER 1 AP seqret CL qanxflatinc-id:X13776 test.out -auto FI stderr FZ = 125 FP /Error: Unable to read sequence 'qanxflatinc-id:X13776'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qapxflat database ############################################# ID dbxflat-swiss-keep DL keep AP dbxflat IN swnew IN swissresource IN IN IN ../../swnew IN IN IN IN FI stderr FC = 13 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxflat FC = 3 FP /^Processing file: .*trembl\.dat entries: 9 \(9\)/ FP 1 /^Processing file: \S+\.dat/ FI swnew.ent FC = 5 FP /# Number of files: 1\n/ FP /[a-z_]+\.dat\n/ FI swnew.xid FZ = 2149 FP /\000o42495_takru\000/ FI swnew.xac FZ = 2143 FP /\000o42495\000/ FI swnew.pxac FZ = 178 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 3\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 9\n/ FP /^Fullcount 9\n/ FP /^Kwlimit 15\n/ FI swnew.pxid FZ = 178 FP /^Type Identifier\n/ FP /^Compress Yes\n/ FP /^Pages 3\n/ FP /^Order 71\n/ FP /^Fill 46\n/ FP /^Pagesize 2048\n/ FP /^Level 0\n/ FP /^Cachesize 100\n/ FP /^Order2 99\n/ FP /^Fill2 101\n/ FP /^Count 9\n/ FP /^Fullcount 9\n/ FP /^Kwlimit 15\n/ // ID dbxflat-swiss-idfirst AP seqret CL qapxflat-id:O42495_TAKRU test.out -auto FI test.out FZ = 471 FP 1 /^>O42495_TAKRU / FP 1 /^>/ // ID dbxflat-swiss-idsecond AP seqret CL qapxflat-id:Q1KKT3_TAKRU test.out -auto FI test.out FZ = 466 FP 1 /^>Q1KKT3_TAKRU / FP 1 /^>/ // ID dbxflat-swiss-last AP seqret CL qapxflat-id:Q68HA9_TAKRU test.out -auto FI test.out FZ = 679 FP 1 /^>Q68HA9_TAKRU / FP 1 /^>/ // ID dbxflat-swiss-nextlast AP seqret CL qapxflat-id:Q50J40_TAKRU test.out -auto FI test.out FZ = 441 FP 1 /^>Q50J40_TAKRU / FP 1 /^>/ // ID dbxflat-swiss-all AP seqret CC Fails to fetch all entries in emboss access method CL "qapxflat:*" test.out -auto FI test.out FZ = 4657 FP 1 /^>Q2KT90_TAKRU / FP 9 /^>/ // ID dbxflat-swiss-wild AP seqret CL "qapxflat:q2*" test.out -auto FI test.out FZ = 957 FP 1 /^>Q2KT90_TAKRU / FP 3 /^>/ // ############################################# # The qanxgcg database(s) ############################################# ID dbxgcg-ex-keep DL keep TI 120 AP dbxgcg IN embl IN emblresource IN embl IN ../../embl IN IN IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxgcg FC = 11 FP 9 /^Processing file: / FP 9 /^Processing file: eem_[a-z1-9]+\.seq / FP 1 /^Processing file: eem_hum1\.seq entries: 32 \(15\) / FI embl.ent FC = 13 FP 1 /^Dual filename database\n/ FP 1 /^# Number of files: 9\n/ FP 9 / eem_[a-z1-9]+\.ref\n/ FI embl.pxac FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 48\n/ FP 1 /^Fullcount 48\n/ FP 1 /^Kwlimit 15\n/ FI embl.pxid FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 40\n/ FP 1 /^Fullcount 40\n/ FP 1 /^Kwlimit 15\n/ FI embl.xac FZ = 2686 FP 1 /\000ab000095\000/ FI embl.xid FZ = 2546 FP 1 /\000x65923\000/ // ID dbxgcg-id AP seqret CL qanxgcg-id:X65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbxgcg-idfirst AP seqret CL qanxgcg-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbxgcg-idsecond AP seqret CL qanxgcg-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbxgcg-last AP seqret CL qanxgcg-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbxgcg-nextlast AP seqret CL qanxgcg-id:Z69719 test.out -auto FI test.out FZ = 34577 FP 1 /^>Z69719 / FP 1 /^>/ // ID dbxgcg-acc AP seqret CL qanxgcg:L07770 test.out -auto FI test.out FZ = 1775 FP 1 /^>L07770 / FP 1 /^>/ // ID dbxgcg-splitfirst AP seqret CL qanxgcg-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbxgcg-splitmid AP seqret CL qanxgcg-id:AL034557 test.out -auto FI test.out FZ = 399267 FP 1 /^>AL034557 / FP 1 /^>/ // ID dbxgcg-splitbefore AP seqret CL qanxgcg-id:AL034557 test.out -auto FI test.out FZ = 399267 FP 1 /^>AL034557 / FP 1 /^>/ // ID dbxgcg-splitafter AP seqret CL qanxgcg-id:AL035476 test.out -auto FI test.out FZ = 326444 FP 1 /^>AL035476 / FP 1 /^>/ // ID dbxgcg-splitend AP seqret CL qanxgcg-id:U18997 test.out -auto FI test.out FZ = 378731 FP 1 /^>U18997 / FP 1 /^>/ // ID dbxgcg-all AP seqret CL "qanxgcg:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>L07770 / FP 40 /^>/ // ID dbxgcg-wild AP seqret CL "qanxgcg:a*" test.out -auto FI test.out FZ = 1251303 FP 3 /^>AB/ FP 9 /^>A/ FP 9 /^>/ // ID dbxgcg-testexc AP seqret CL qanxgcgexc-id:x65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbxgcg-testexcall AP seqret CL "qanxgcgexc-id:*" test.out -auto FI test.out FZ = 1744803 FP 1 /^>X65923 / FP 30 /^>/ // ID dbxgcg-testexcfail ER 1 AP seqret CL qanxgcgexc-id:j01636 test.out -auto FI stderr FZ = 124 FP /Error: Unable to read sequence 'qanxgcgexc-id:j01636'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbxgcg-testinc AP seqret CL qanxgcginc-id:j01636 test.out -auto FI test.out FZ = 7677 FP 1 /\A>J01636 / FP 1 /^>/ // ID dbxgcg-testincall AP seqret CL "qanxgcginc-id:*" test.out -auto FI test.out FZ = 400271 FP 1 /^>J01636 / FP 10 /^>/ // ID dbxgcg-testincfail ER 1 AP seqret CL qanxgcginc-id:x65923 test.out -auto FI stderr FZ = 124 FP /Error: Unable to read sequence 'qanxgcginc-id:x65923'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qangcgall database(s) ############################################# ID dbxgcg-allsys-keep DL keep TI 120 AP dbxgcg CL -fields "id,acc,sv,des,key,org" IN embl IN emblresource IN embl IN ../../embl IN IN IN FI stderr FC = 6 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI outfile.dbxgcg FC = 11 FP 9 /^Processing file: / FP 9 /^Processing file: eem_[a-z1-9]+\.seq / FP 1 /^Processing file: eem_hum1\.seq entries: 32 \(15\) / FI embl.ent FC = 13 FP 1 /^Dual filename database\n/ FP 1 /^# Number of files: 9\n/ FP 9 / eem_[a-z1-9]+\.ref\n/ FI embl.pxac FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 48\n/ FP 1 /^Fullcount 48\n/ FP 1 /^Kwlimit 15\n/ FI embl.pxde FZ = 183 FP 1 /^Type Secondary\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 615\n/ FP 1 /^Order 60\n/ FP 1 /^Fill 41\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 202\n/ FP 1 /^Fullcount 381\n/ FP 1 /^Kwlimit 20\n/ FI embl.pxid FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 40\n/ FP 1 /^Fullcount 40\n/ FP 1 /^Kwlimit 15\n/ FI embl.pxkw FZ = 181 FP 1 /^Type Secondary\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 176\n/ FP 1 /^Order 31\n/ FP 1 /^Fill 25\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 57\n/ FP 1 /^Fullcount 72\n/ FP 1 /^Kwlimit 50\n/ FI embl.pxsv FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 24\n/ FP 1 /^Fullcount 24\n/ FP 1 /^Kwlimit 15\n/ FI embl.pxtx FZ = 182 FP 1 /^Type Secondary\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 303\n/ FP 1 /^Order 46\n/ FP 1 /^Fill 34\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 99\n/ FP 1 /^Fullcount 434\n/ FP 1 /^Kwlimit 30\n/ FI embl.xac FZ = 2686 FP 1 /\000ab000095\000/ FI embl.xde FZ = 33004 FP 1 /\000fau\000/ FI embl.xid FZ = 2546 FP 1 /\000x65923\000/ FI embl.xkw FZ = 10964 FP 2 /\000dna_binding_protein\000/ FI embl.xsv FZ = 2718 FP 1 /\000ab000095\.1\000/ FI embl.xtx FZ = 20707 FP 1 /\000mus\000/ // ID dbxgcg-allsys-id AP seqret CL qanxgcgall-id:x65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbxgcg-allsys-idfirst AP seqret CL qanxgcgall-id:AB000095 test.out -auto FI test.out FZ = 2542 FP 1 /^>AB000095 / FP 1 /^>/ // ID dbxgcg-allsys-idsecond AP seqret CL qanxgcgall-id:AB009062 test.out -auto FI test.out FZ = 594 FP 1 /^>AB009062 / FP 1 /^>/ // ID dbxgcg-allsys-last AP seqret CL qanxgcgall-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbxgcg-allsys-nextlast AP seqret CL qanxgcgall-id:Z69719 test.out -auto FI test.out FZ = 34577 FP 1 /^>Z69719 / FP 1 /^>/ // ID dbxgcg-allsys-acc AP seqret CL qanxgcgall:L07770 test.out -auto FI test.out FZ = 1775 FP 1 /^>L07770 / FP 1 /^>/ // ID dbxgcg-allsys-splitfirst AP seqret CL qanxgcgall-id:Z95399 test.out -auto FI test.out FZ = 362910 FP 1 /^>Z95399 / FP 1 /^>/ // ID dbxgcg-allsys-splitmid AP seqret CL qanxgcgall-id:AL034557 test.out -auto FI test.out FZ = 399267 FP 1 /^>AL034557 / FP 1 /^>/ // ID dbxgcg-allsys-splitbefore AP seqret CL qanxgcgall-id:AC017364 test.out -auto FI test.out FZ = 3801 FP 1 /^>AC017364 / FP 1 /^>/ // ID dbxgcg-allsys-splitafter AP seqret CL qanxgcgall-id:AL035476 test.out -auto FI test.out FZ = 326444 FP 1 /^>AL035476 / FP 1 /^>/ // ID dbxgcg-allsys-splitend AP seqret CL qanxgcgall-id:AL035476 test.out -auto FI test.out FZ = 326444 FP 1 /^>AL035476 / FP 1 /^>/ // ID dbxgcg-allsys-all AP seqret CL "qanxgcgall:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbxgcg-allsys-wild AP seqret CL "qanxgcgall:a*" test.out -auto FI test.out FZ = 1251303 FP 9 /^>A/ FP 3 /^>AB/ FP 9 /^>/ // ID dbxgcg-allsys-acnum AP seqret CL qanxgcgall-acc:X65923 test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbxgcg-allsys-acnumall AP seqret CL "qanxgcgall-acc:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbxgcg-allsys-acnumwild AP seqret CL "qanxgcgall-acc:x*" test.out -auto FI test.out FZ = 18988 FP 11 /^>[A-Z0-9]+ X/ FP 11 /^>/ // ID dbxgcg-allsys-sv AP seqret CL qanxgcgall-sv:D00596.1 test.out -auto FI test.out FZ = 19008 FP 1 /^>D00596 / FP 1 /^>/ // ID dbxgcg-allsys-svall AP seqret CL "qanxgcgall-sv:*" test.out -auto FI test.out FZ = 2066925 FP 1 /^>D00596 / FP 0 /^>X65923 / FP 24 /^>/ // ID dbxgcg-allsys-svwild AP seqret CL "qanxgcgall-sv:x*" test.out -auto FI test.out FZ = 5043 FP 3 /^>X/ FP 3 /^>/ // ID dbxgcg-allsys-des AP seqret CL qanxgcgall-des:fau test.out -auto FI test.out FZ = 561 FP 1 /\A>X65923 / FP 1 /^>/ // ID dbxgcg-allsys-desall AP seqret CL "qanxgcgall-des:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbxgcg-allsys-deswild AP seqret CL "qanxgcgall-des:m*" test.out -auto FI test.out FZ = 1543931 FP 18 /^>.* [Mm]/ FP 18 /^>/ // ID dbxgcg-allsys-key AP seqret CL qanxgcgall-key:rhodopsin test.out -auto FI test.out FZ = 5086 FP 1 /^>L07770 / FP 3 /^>/ // ID dbxgcg-allsys-keyall AP seqret CL "qanxgcgall-key:*" test.out -auto FI test.out FZ = 1470428 FP 1 /^>L07770 / FP 35 /^>/ // ID dbxgcg-allsys-keywild AP seqret CL "qanxgcgall-key:m*" test.out -auto FI test.out FZ = 9919 FP 1 /^>AB009602/ FP 3 /^>/ // ID dbxgcg-allsys-keyspace AP seqret CL "qanxgcgall-key:lacy gene" test.out -osformat embl -auto FI test.out FZ = 26226 FP 2 /^KW .*; lacY gene;/ FP 2 /^ID / // ID dbxgcg-allsys-org AP seqret CL qanxgcgall-org:Mus test.out -auto FI test.out FZ = 475 FP 1 /^>L48662 / FP 1 /^>/ // ID dbxgcg-allsys-orgall AP seqret CL "qanxgcgall-org:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbxgcg-allsys-orgwild AP seqret CL "qanxgcgall-org:*" test.out -auto FI test.out FZ = 2145074 FP 1 /^>X13776 / FP 40 /^>/ // ID dbxgcg-allsys-orgwild2 AP seqret CL "qanxgcgall-org:mus*" test.out -auto FI test.out FZ = 4276 FP 1 /^>L48662/ FP 2 /^>/ // ############################################# # The qaxpir database(s) ############################################# ID dbxgcg-pir-keep DL keep TI 120 AP dbxgcg IN pir IN pirresource IN pir IN ../../pir IN IN IN IN FI stderr FC = 12 FP 0 /Warning:/ FP 0 /Error: / FP 0 /Died: / FI outfile.dbxgcg FC = 6 FP 4 /^Processing file: / FP 4 /^Processing file: pir[1-9]\.seq / FP 1 /^Processing file: pir3\.seq entries: 57 \(3\) / FI pir.ent FC = 8 FP 1 /^# Number of files: 4\n/ FP 1 /^Dual filename database\n/ FP 4 /^pir[1-9]\.seq pir[1-9]\.ref\n/ FI pir.pxac FZ = 181 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 25\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 78\n/ FP 1 /^Fullcount 93\n/ FP 1 /^Kwlimit 15\n/ FI pir.pxid FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 60\n/ FP 1 /^Fullcount 60\n/ FP 1 /^Kwlimit 15\n/ FI pir.xac FZ = 6064 FP 1 /\000a00011\000/ FP 1 /\000a04607\000/ FI pir.xid FZ = 3018 FP 1 /\000ccms\000/ FP 2 /\000cchu\000/ // ID dbxgcg-pir-id AP seqret CL qaxpir-id:cchu test.out -auto FI test.out FZ = 153 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbxgcg-pir-idfirst AP seqret CL qaxpir-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbxgcg-pir-idsecond AP seqret CL qaxpir-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbxgcg-pir-last AP seqret CL qaxpir-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbxgcg-pir-nextlast AP seqret CL qaxpir-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbxgcg-pir-acc AP seqret CL qaxpir:A00001 test.out -auto FI test.out FZ = 153 FP 1 /^>CCHU / FP 1 /^>/ // ID dbxgcg-pir-all AP seqret CL "qaxpir:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>S11172 / FP 60 /^>/ // ID dbxgcg-pir-wild AP seqret CL "qaxpir:c*" test.out -auto FI test.out FZ = 7969 FP 49 /^>C/ FP 49 /^>/ // ID dbxgcg-pir-testexc AP seqret CL qaxpirexc-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /\A>S11172 / FP 1 /^>/ // ID dbxgcg-pir-testexcall AP seqret CL "qaxpirexc-id:*" test.out -auto FI test.out FZ = 2498 FP 1 /^>S11172 / FP 11 /^>/ // ID dbxgcg-pir-testexcfail ER 1 AP seqret CL qaxpirexc-id:cchu test.out -auto FI stderr FZ = 121 FP /Error: Unable to read sequence 'qaxpirexc-id:cchu'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID dbxgcg-pir-testinc AP seqret CL qaxpirinc-id:cchu test.out -auto FI test.out FZ = 153 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbxgcg-pir-testincall AP seqret CL "qaxpirinc-id:*" test.out -auto FI test.out FZ = 7969 FP 1 /^>CCHU / FP 49 /^>/ // ID dbxgcg-pir-testincfail ER 1 AP seqret CL qaxpirinc-id:S11172 test.out -auto FI stderr FZ = 123 FP /Error: Unable to read sequence 'qaxpirinc-id:S11172'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ############################################# # The qapirall database(s) ############################################# # fields seqvn not supported by PIR format data ID dbxgcg-pirall-keep DL keep TI 120 AP dbxgcg CL -fields "id,acc,des,key,org" IN pir IN pirresource IN pir IN ../../pir IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxgcg FC = 6 FP 4 /^Processing file: / FP 4 /^Processing file: pir[1-9]\.seq / FP 1 /^Processing file: pir3\.seq entries: 57 \(3\) / FI pir.ent FC = 8 FP 1 /^# Number of files: 4\n/ FP 1 /^Dual filename database\n/ FP 4 /^pir[1-9]\.seq pir[1-9]\.ref\n/ FI pir.pxac FZ = 181 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 25\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 78\n/ FP 1 /^Fullcount 93\n/ FP 1 /^Kwlimit 15\n/ FI pir.pxde FZ = 183 FP 1 /^Type Secondary\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 413\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 136\n/ FP 1 /^Fullcount 319\n/ FP 1 /^Kwlimit 15\n/ FI pir.pxid FZ = 180 FP 1 /^Type Identifier\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 3\n/ FP 1 /^Order 71\n/ FP 1 /^Fill 46\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 99\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 60\n/ FP 1 /^Fullcount 60\n/ FP 1 /^Kwlimit 15\n/ FI pir.pxkw FZ = 181 FP 1 /^Type Secondary\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 51\n/ FP 1 /^Order 52\n/ FP 1 /^Fill 37\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 16\n/ FP 1 /^Fullcount 474\n/ FP 1 /^Kwlimit 25\n/ FI pir.pxtx FZ = 183 FP 1 /^Type Secondary\n/ FP 1 /^Compress Yes\n/ FP 1 /^Pages 331\n/ FP 1 /^Order 41\n/ FP 1 /^Fill 31\n/ FP 1 /^Pagesize 2048\n/ FP 1 /^Level 0\n/ FP 1 /^Cachesize 100\n/ FP 1 /^Order2 71\n/ FP 1 /^Fill2 101\n/ FP 1 /^Count 108\n/ FP 1 /^Fullcount 117\n/ FP 1 /^Kwlimit 35\n/ FI pir.xac FZ = 6064 FP 1 /\000a00011\000/ FP 1 /\000a04607\000/ FI pir.xde FZ = 22961 FP 1 /\000fragments\000/ FP 2 /\000fragment/ FI pir.xid FZ = 3018 FP 1 /\000ccms\000/ FP 2 /\000cchu\000/ FI pir.xkw FZ = 8842 FP 1 /\000heme\000/ FI pir.xtx FZ = 18417 FP 2 /\000domestic_sheep\000/ FP 1 /\000domestic_duck\000/ FP 1 /\000equus_quagga\000/ // ID dbxgcg-pirall-id AP seqret CL qaxpirall-id:cchu test.out -auto FI test.out FZ = 153 FP 1 /\A>CCHU / FP 1 /^>/ // ID dbxgcg-pirall-idfirst AP seqret CL qaxpirall-id:A31558 test.out -auto FI test.out FZ = 156 FP 1 /^>A31558 / FP 1 /^>/ // ID dbxgcg-pirall-idsecond AP seqret CL qaxpirall-id:A32902 test.out -auto FI test.out FZ = 123 FP 1 /^>A32902 / FP 1 /^>/ // ID dbxgcg-pirall-last AP seqret CL qaxpirall-id:S29350 test.out -auto FI test.out FZ = 186 FP 1 /^>S29350 / FP 1 /^>/ // ID dbxgcg-pirall-nextlast AP seqret CL qaxpirall-id:S11172 test.out -auto FI test.out FZ = 178 FP 1 /^>S11172 / FP 1 /^>/ // ID dbxgcg-pirall-acc AP seqret CL qaxpirall:A00001 test.out -auto FI test.out FZ = 153 FP 1 /^>CCHU / FP 1 /^>/ // ID dbxgcg-pirall-all AP seqret CL "qaxpirall:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>S11172 / FP 60 /^>/ // ID dbxgcg-pirall-wild AP seqret CL "qaxpirall:c*" test.out -auto FI test.out FZ = 7969 FP 49 /^>C/ FP 49 /^>/ // ID dbxgcg-pirall-acnum AP seqret CL qaxpirall-acc:A04605 test.out -auto FI test.out FZ = 151 FP 1 /\A>CCRT / FP 1 /^>/ // ID dbxgcg-pirall-acnumall AP seqret CL "qaxpirall-acc:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>CCHU / FP 1 /^>CCRT / FP 60 /^>/ // ID dbxgcg-pirall-acnumwild AP seqret CL "qaxpirall-acc:s*" test.out -auto FI test.out FZ = 841 ## CCHO has an S* secondary accession number, rest are primary FP 4 /^>[A-Z0-9]+ S/ FP 5 /^>/ // ID dbxgcg-pirall-des AP seqret CL qaxpirall-des:cytochrome test.out -auto FI test.out FZ = 8825 FP 1 /^>CCHU / FP 54 /^>/ // ID dbxgcg-pirall-desall AP seqret CL "qaxpirall-des:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>CCHU / FP 60 /^>/ // ID dbxgcg-pirall-deswild AP seqret CL "qaxpirall-des:p*" test.out -auto FI test.out FZ = 2399 FP 11 /^>.*[ -][Pp]/ FP 11 /^>/ // ID dbxgcg-pirall-key AP seqret CL qaxpirall-key:polymorphism test.out -auto FI test.out FZ = 153 FP 1 /^>CCHU / FP 1 /^>/ // ID dbxgcg-pirall-keyall AP seqret CL "qaxpirall-key:*" test.out -auto FI test.out FZ = 9109 FP 1 /^>CCHU / FP 56 /^>/ // # only entries with keywords ID dbxgcg-pirall-keyall2 AP seqret CL "qaxpirall-key:?*" test.out -auto FI test.out FZ = 9109 FP 1 /^>CCHU / FP 56 /^>/ // ID dbxgcg-pirall-keyspace AP entret CL "qaxpirall-key:blocked amino end" test.out -auto FI test.out FZ = 11846 FP 1 /^>P1;CCRT/ FP 8 /^>/ FP 8 /^C;Keywords:.*blocked amino end;/ // ID dbxgcg-pirall-keywild AP seqret CL "qaxpirall-key:m*" test.out -auto FI test.out FZ = 8825 FP 1 /^>CCHU / FP 54 /^>/ // ID dbxgcg-pirall-org AP seqret CL "qaxpirall-org:drosophila melanogaster" test.out -auto FI test.out FZ = 180 FP 1 /^>CCFFDM / FP 1 /^>/ // ID dbxgcg-pirall-orgall AP seqret CL "qaxpirall-org:*" test.out -auto FI test.out FZ = 10467 FP 1 /^>CCHU / FP 60 /^>/ // ID dbxgcg-pirall-orgwild AP seqret CL "qaxpirall-org:s*" test.out -auto FI test.out FZ = 2010 FP 1 /^>CCPG / FP 12 /^>/ // ID dbxgcg-pirall-orgwild2 AP seqret CL "qaxpirall-org:mus*" test.out -auto FI test.out FZ = 324 FP 1 /^>CCMS / FP 2 /^>/ // ID dbxstat-ex AP dbxstat IN edam IN ns IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edam.dbxstat FC = 9 FP 7 /^ +\d+ [a-z]+\n/ // ID dbxedam-keep AP dbxedam DL keep IN IN IN IN ../../data/ IN IN IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxedam FC = 3 FP 1 /Processing file: / FI edam.ent FC = 5 FP 1 /Single filename database\n/ FP /EDAM.obo\n/ FI edam.pxac FC = 13 FP /^Count +153\n/ FP /^Fullcount +153\n/ FI edam.pxde FC = 13 FP /^Count +515\n/ FP /^Fullcount +1611\n/ FI edam.pxhasin FC = 13 FP /^Count +3\n/ FP /^Fullcount +3\n/ FI edam.pxhasout FC = 13 FP /^Count +4\n/ FP /^Fullcount +7\n/ FI edam.pxid FC = 13 FP /^Count +144\n/ FP /^Fullcount +144\n/ FI edam.pxis FC = 13 FP /^Count +75\n/ FP /^Fullcount +230\n/ FI edam.pxisfmt FC = 13 FP /^Count +7\n/ FP /^Fullcount +20\n/ FI edam.pxisid FC = 13 FP /^Count +1\n/ FP /^Fullcount +1\n/ FI edam.pxnm FC = 13 FP /^Count +204\n/ FP /^Fullcount +425\n/ FI edam.pxns FC = 13 FP /^Count +6\n/ FP /^Fullcount +144\n/ FI edam.xac FZ = 14559 FP 2 /sequence_reformatting/ FI edam.xde FZ = 91681 FP 2 /dependent/ FI edam.xhasin FZ = 2564 FP 2 /0000849/ FI edam.xhasout FZ = 2744 FP 2 /0002044/ FI edam.xid FZ = 6428 FP 2 /0000607/ FI edam.xis FZ = 14828 FP 2 /0002065/ FI edam.xisfmt FZ = 3236 FP 2 /0000925/ FI edam.xisid FZ = 2276 FP 2 /0000006/ FI edam.xnm FZ = 34366 FP 2 /\000cliques\000/ FI edam.xns FZ = 3581 FP 2 /entity/ FP 2 /\0000000002\000/ // ID dbxedam-idfirst AP ontoget CL tedam:0000002 -obsolete IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FP /^id: TEDAM:0000002\n/ FP 1 /^id: / FP 0 /^is_a: EDAM:/ FP 0 /^relationship: / FC = 7 // ID dbxedam-idlast AP ontoget CL tedam:0003001 IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FP /^id: TEDAM:0003001\n/ FP 1 /^id: / FP 1 /^is_a: EDAM:0002330/ FP 1 /^relationship: / FC = 9 // ID dbxobo-keep AP dbxobo DL keep IN edam IN IN oboresource IN ../../data/ IN EDAM.obo IN * IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxobo FC = 3 FP 1 /Processing file: / FI edam.ent FC = 5 FP 1 /Single filename database\n/ FP /EDAM.obo\n/ FI edam.pxac FC = 13 FP /^Count +153\n/ FP /^Fullcount +153\n/ FI edam.pxde FC = 13 FP /^Count +515\n/ FP /^Fullcount +1611\n/ FI edam.pxid FC = 13 FP /^Count +144\n/ FP /^Fullcount +144\n/ FI edam.pxis FC = 13 FP /^Count +75\n/ FP /^Fullcount +230\n/ FI edam.pxnm FC = 13 FP /^Count +204\n/ FP /^Fullcount +425\n/ FI edam.pxns FC = 13 FP /^Count +6\n/ FP /^Fullcount +144\n/ FI edam.xac FZ = 23400 FP 2 /nucleic_acid_data/ FI edam.xde FZ = 91915 FP 2 /discipline/ FI edam.xid FZ = 6428 FP 2 /0000607/ FI edam.xis FZ = 14828 FP 2 /0002065/ FI edam.xnm FZ = 40367 FP 2 /\000jaspar\000/ FI edam.xns FZ = 3581 FP 2 /entity/ FP 2 /\0000000002\000/ // ID dbxobo-idfirst AP ontoget CL tobo:0000002 -obsolete IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FP /^id: TOBO:0000002\n/ FP 1 /^id: / FP 0 /^is_a: EDAM:/ FP 0 /^relationship: / FC = 7 // ID dbxobo-idlast AP ontoget CL tobo:0003001 IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FP /^id: TOBO:0003001\n/ FP 1 /^id: / FP 1 /^is_a: EDAM:0002330/ FP 1 /^relationship: / FC = 9 // ID dbxresource-keep AP dbxresource DL keep CL drcat IN drcat IN drcatresource IN ../../data/ IN DRCAT.dat IN IN IN FI stderr FC = 20 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP 0 /No '[^']+' index found/ FI drcat.ent FC = 5 FP 1 /[A-z]*\.dat$/ FI drcat.pxac FC = 13 FP /^Count +21\n/ FP /^Fullcount +21\n/ FI drcat.pxcat FC = 13 FP /^Count +19\n/ FP /^Fullcount +72\n/ FI drcat.pxde FC = 13 FP /^Count +835\n/ FP /^Fullcount +2001\n/ FI drcat.pxedat FC = 13 FP /^Count +65\n/ FP /^Fullcount +150\n/ FI drcat.pxefmt FC = 13 FP /^Count +11\n/ FP /^Fullcount +135\n/ FI drcat.pxeid FC = 13 FP /^Count +108\n/ FP /^Fullcount +197\n/ FI drcat.pxetpc FC = 13 FP /^Count +67\n/ FP /^Fullcount +204\n/ FI drcat.pxid FC = 13 FP /^Count +110\n/ FP /^Fullcount +110\n/ FI drcat.pxnm FC = 13 FP /^Count +335\n/ FP /^Fullcount +659\n/ FI drcat.pxqfmt FC = 13 FP /^Count +16\n/ FP /^Fullcount +148\n/ FI drcat.pxqin FC = 13 FP /^Count +122\n/ FP /^Fullcount +204\n/ FI drcat.pxqout FC = 13 FP /^Count +126\n/ FP /^Fullcount +169\n/ FI drcat.pxqurl FC = 13 FP /^Count +737\n/ FP /^Fullcount +2118\n/ FI drcat.pxrest FC = 13 FP /^Count +12\n/ FP /^Fullcount +43\n/ FI drcat.pxrf FC = 13 FP /^Count +4\n/ FP /^Fullcount +87\n/ FI drcat.pxsoap FC = 13 FP /^Count +18\n/ FP /^Fullcount +23\n/ FI drcat.pxtaxid FC = 13 FP /^Count +26\n/ FP /^Fullcount +114\n/ FI drcat.pxurl FC = 13 FP /^Count +231\n/ FP /^Fullcount +594\n/ FI drcat.xac FZ = 2437 FP 2 /\000eupathdb\000/ FI drcat.xcat FZ = 5915 FP 2 /\0002d_gel_databases\000/ FI drcat.xde FZ = 138441 FP 2 /\000alternative\000/ FI drcat.xedat FZ = 12590 FP 2 /\0000002360\000/ FI drcat.xefmt FZ = 5347 FP 2 /\0000002331\000/ FI drcat.xeid FZ = 18816 FP 2 /\0000001179\000/ FI drcat.xetpc FZ = 13630 FP 2 /\0000000719\000/ FI drcat.xid FZ = 5809 FP 2 /\000cath\000/ FI drcat.xnm FZ = 56362 FP 2 /\000cornea\000/ FI drcat.xqfmt FZ = 6182 FP 2 /\000html\000/ FI drcat.xqin FZ = 22292 FP 2 /\000genbank_identifier\000/ FI drcat.xqout FZ = 25066 FP 2 /\000domain_motif_interaction\000/ FI drcat.xqurl FZ = 128181 FP 2 /\000burnham\000/ FI drcat.xrest FZ = 4366 FP 2 /\000jsp\000/ FI drcat.xrf FZ = 3751 FP 2 /\000sp_explicit\000/ FI drcat.xsoap FZ = 4705 FP 2 /\000soap2\000/ FI drcat.xtaxid FZ = 7112 FP 2 /\0001\000/ FI drcat.xurl FZ = 40655 FP 2 /\000biochem\000/ FI outfile.dbxresource FC = 3 FP 1 /Processing file: / // ID dbxtax-keep AP dbxtax DL keep TI 1200 IN IN IN ../../data/taxonomy IN IN IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.dbxtax FC = 3 FP 1 /Processing file: / FI taxon.ent FC = 5 FP 1 /Dual filename database\n/ FP /nodes.dmp names.dmp\n/ FI taxon.pxac FC = 13 FP /^Count +1\n/ FP /^Fullcount +1\n/ FI taxon.pxgc FC = 13 FP /^Count +1\n/ FP /^Fullcount +41\n/ FI taxon.pxid FC = 13 FP /^Count +41\n/ FP /^Fullcount +41\n/ FI taxon.pxmgc FC = 13 FP /^Count +3\n/ FP /^Fullcount +39\n/ FI taxon.pxtax FC = 13 FP /^Count +86\n/ FP /^Fullcount +90\n/ FI taxon.pxrnk FC = 13 FP /^Count +17\n/ FP /^Fullcount +41\n/ FI taxon.pxup FC = 13 FP /^Count +33\n/ FP /^Fullcount +41\n/ FI taxon.xac FZ = 2142 FP 2 /\00040673\000/ FI taxon.xgc FZ = 2258 FP 1 /\0009605\0009606\000/ FI taxon.xid FZ = 2138 FP 2 /\0001\000/ FI taxon.xmgc FZ = 2745 FP 1 /\0009605\0009606\000/ FI taxon.xtax FZ = 6298 FP 2 /\000chordata\000/ FI taxon.xrnk FZ = 4753 FP 2 /no_rank/ FI taxon.xup FZ = 3882 FP 2 /\0001\000/ // ID dbxuncompress-keep DL keep AP dbxuncompress PP cp ../dbxflat-all-keep/*de . CL embl -indexdir . -field des IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP 0 /No '[^']+' index found/ FI embl.pxde FC = 13 FP /Compress No\n/ FI embl.xde FZ = 1325056 FP 2 /\000complement\000/ FI embl.dbxuncompress FC = 3 FP /Index 'des' uncompressed\n/ // ID dbxcompress-ex AP dbxcompress PP cp ../dbxuncompress-keep/*de . CL embl -indexdir . -field des IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP 0 /No '[^']+' index found/ FI embl.pxde FC = 13 FP /Compress Yes\n/ FI embl.xde FZ = 34946 FP 2 /\000complement\000/ FI embl.dbxcompress FC = 3 FP /Index 'des' opened, compressing\n/ // ################################################################## # end of database access tests ################################################################## ID dbtell-ex AP dbtell CL tsw FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 19 FP /^DBNAME tsw \[\n/ FP 6 /^ field: / FP 1 /^ field: "id"\n/ // ID dbxreport-ex PP cp ../dbxflat-ex-keep/embl.*ac . PP cp ../dbxflat-ex-keep/embl.*id . AP dbxreport CL -indexdir . IN embl IN id,acc IN QQ rm embl.xac QQ rm embl.pxac QQ rm embl.xid QQ rm embl.pxid FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP 0 /No '[^']+' index found/ FI embl.dbxreport FC = 55 FP 2 /Identifier index '[^']+' index found with \d+ pages/ // ID degapseq-ex AP degapseq CL ../../data/dnagap.fasta nogaps.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI nogaps.seq FZ = 138 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID descseq-ex UC Set the name of a sequence to "myclone23" AP descseq CL -seq ../../data/dna.text -out clone23.seq -name "myclone23" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI clone23.seq FZ = 113 FP /^>myclone23\n/ // ID descseq-ex2 UC Set the description of a sequence to "This is my clone number 244" AP descseq CL -seq ../../data/dna.text -out xy24.seq -desc "This is my clone number 244" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI xy24.seq FZ = 142 FP /EMBOSS_001 This is my clone number 244\n/ // ID descseq-ex3 UC Append some text to the description of a sequence AP descseq CL -seq ../../data/dna.text -out est4.seq -desc " (submitted)" -append FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI est4.seq FZ = 127 FP /EMBOSS_001 \(submitted\)\n/ // ID diffseq-ex AP diffseq CL tembl:x65923 tembl:ay411291 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.diffseq FZ = 1571 FP /^# X65923 overlap starts at 57\n/ FP /^# AY411291 overlap starts at 1\n/ FP /^X65923 284-284 Length: 1\n/ FP /^Sequence: c\nFeature: gene 1-402 gene='FAU' locus_tag='HCM4175'\n/ FP /^# Overlap_end: 458 in X65923\n/ FP /^# Overlap_end: 402 in AY411291\n/ FI AY411291.diffgff FC = 6 FP /^AY411291\tdiffseq\tsequence_conflict\t228\t228\t1\.000\t[+]\t\.\tID=AY411291\.1;note=SNP in X65923;replace=t/ FI X65923.diffgff FC = 6 FP /^X65923\tdiffseq\tsequence_conflict\t284\t284\t1\.000\t[+]\t\.\tID=X65923\.1;note=SNP in AY411291;replace=c\n/ // ID distmat-ex AP distmat CC Example file missing test/data/pax.align CC No example in the documentation CL ../../data/pax.align IN 2 IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax.distmat FP / Kimura / FP /^\s+0\.00\s+20\.37\s+PX8A_HUMAN 9\n/ FC = 17 // ID dotmatcher-ex AP dotmatcher CL tsw:hba_human tsw:hbb_human -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dotmatcher.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 22 FP /^Created dotmatcher\.ps\n/ // ID dotmatcher-data AP dotmatcher CL tsw:hba_human tsw:hbb_human -graph data FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Created dotmatcher1\.dat\n/ FI dotmatcher1.dat FC = 30 FP /^##Maintitle Dotmatcher: tsw-id:HBA_HUMAN vs tsw-id:HBB_HUMAN\n/ FP /^##Subtitle \(windowsize = 10, threshold = 23.00 \d\d\/\d\d\/[0-9][0-9]\)\n/ FP /^Text2 x1 71\.000000 y1 -11\.025001 colour 0 size 1\.000000 HBA_HUMAN\n/ // ID dotmatcher-stretchdata AP dotmatcher CL tsw:hba_human tsw:hbb_human -stretch -xygraph data FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /Created dotmatcher1\.dat\n/ FI dotmatcher1.dat FC = 27 FP /^##Title Dotmatcher: tsw-id:HBA_HUMAN vs tsw-id:HBB_HUMAN\n/ FP /^##XminA 1\.000000 XmaxA 142\.000000 YminA 1\.000000 YmaxA 147\.000000\n/ FP /^##Xmin 1\.000000 Xmax 142\.000000 Ymin 1\.000000 Ymax 147\.000000\n/ FP /^##ScaleXmin 1\.000000 ScaleXmax 142\.000000 ScaleYmin 1\.000000 ScaleYmax 147\.000000\n/ FP /^##Maintitle \(windowsize = 10, threshold = 23\.00 [0-9\/]+\)\n/ FP /^Line x1 80\.000000 y1 68\.000000 x2 90\.000000 y2 78\.000000 colour 0\n/ FP /^##GraphObjects\n/ FP /^##Number 0\n/ // ID dotmatcher-stretch AP dotmatcher CL tsw:hba_human tsw:hbb_human -xygraph ps -stretch IN FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 22 FP /^Created dotmatcher\.ps\n/ FI dotmatcher.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID dotpath-ex AP dotpath ## ## timeout 60 seconds on original test system ## TI 400 CL tembl:AF129756 tembl:BA000025 -word 20 -graph cps -overlaps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created dotpath\.ps\n/ FI dotpath.ps FZ > 16600 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID dotpath-data AP dotpath ## ## timeout 60 seconds on original test system ## TI 400 CL tembl:AF129756 tembl:BA000025 -word 20 -graph data FI dotpath1.dat FC = 254 FP /^##Maintitle Dotpath: tembl-id:AF129756 vs tembl-id:BA000025\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^Line x1 1\.000000 y1 193957\.000000 x2 153\.000000 y2 194109\.000000 colour 0\n/ FI stdout FC = 1 FP /^Created dotpath1\.dat\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-ex AP dottup CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -graph cps FI stdout FZ = 18 FP /^Created dottup\.ps\n/ FI dottup.ps FC = 2529 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-data AP dottup CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" CL -graph data IN FI stdout FC = 1 FP /^Created dottup1\.dat\n/ FI dottup1.dat FC = 2284 FP /^##Maintitle v00294 vs j01636\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^Line x1 5288\.000000 y1 625\.000000 x2 5298\.000000 y2 635\.000000 colour 0\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-stretchdata AP dottup CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" CL -stretch -xygraph data IN FI stdout FC = 1 FP /^Created dottup1\.dat\n/ FI dottup1.dat FC = 2265 FP /^Line x1 5510\.000000 y1 195\.000000 x2 5521\.000000 y2 206\.000000 colour 0\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dottup-stretch AP dottup CL tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -xygraph ps CL -stretch IN FI stdout FZ = 18 FP /^Created dottup\.ps\n/ FI dottup.ps FZ > 66990 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dreg-ex AP dreg IN tembl:x13776 IN ggtacc IN FI x13776.dreg FC = 31 FP / 1 6 [+] regex: GGTACC ggtacc\n/ FP 1 /^# Reported_sequences: 1\n/ FP 1 /^# Reported_hitcount: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dreg-test-fwd AP dreg CL -rformat listfile IN asis::caaggttccaacc IN aa IN test.out FI test.out FC = 33 FP 2 /^asis::/ FP 1 /^asis::caaggttccaacc\[2\:3\]\n/ FP 1 /^asis::caaggttccaacc\[10\:11\]\n/ FP 1 /^# Reported_sequences: 1\n/ FP 1 /^# Reported_hitcount: 2\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID dreg-test-rev AP dreg CL -rformat listfile -srev IN asis::caaggttccaacc IN aa IN test.out FI test.out FC = 33 FP 1 /^asis::/ FP 1 /^asis::caaggttccaacc\[6:7\:r\]\n/ FP 1 /^# Reported_sequences: 1\n/ FP 1 /^# Reported_hitcount: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID drfinddata-ex AP drfinddata CL virus IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI drfinddata.drcat FC = 33 FP 2 /^ID / FP 2 /^EDAMdat 0002307 \| Virus annotation\n/ FP 1 /^EDAMdat 0002308 \| Virus annotation \(taxonomy\)\n/ FP 2 /^Taxon 10239 \| Viruses\n/ // ID drfindformat-ex AP drfindformat CL fasta IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI drfindformat.drcat FC = 210 FP 8 /^ID / FP 6 /^EDAMfmt 0001929 \| FASTA format\n/ FP 2 /^EDAMfmt 0002310 \| FASTA-HTML\n/ FP 8 /^Taxon / FP 7 /^Taxon 1 / // ID drfindid-ex AP drfindid CL protein IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI drfindid.drcat FC = 2066 FP 106 /^ID / // ID drfindresource-ex AP drfindresource CL pathogen IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI drfindresource.drcat FC = 242 FP 15 /^ID \S+\n/ FP 15 /^EDAMtpc 0000783 \| Pathogen\n/ // ID drget-ex AP drget CL drcat:uniprot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI uniprot.drcat FC = 22 FP 1 /^ID \S+\n/ FP 1 /^IDalt UniProtKB\n/ FP 1 /^EDAMtpc 0000639 \| Protein sequences\n/ // ID drtext-ex AP drtext CL drcat:uniprot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI uniprot.drtext FC = 21 FP 1 /^ID \S+\n/ FP 1 /^IDalt UniProtKB\n/ FP 1 /^EDAMtpc 0000639 \| Protein sequences\n/ // ID edamdef-ex AP edamdef CL multiple IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamdef.obo FP /^id: EDAM:0001234\n/ FC = 239 FP 26 /^id: / FP 23 /^def: .*multiple / FP 2 /^def: .*multiple\)/ FP 2 /^def: Multiple / // ID edamdef-ex2 AP edamdef CL multiple -subclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamdef.obo FC = 448 FP /^id: EDAM:0001234\n/ FP 49 /^id: / FP 23 /^def: .*multiple / FP 2 /^def: .*multiple\)/ FP 2 /^def: Multiple / // ID edamdef-nosub AP edamdef CL multiple -nosubclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamdef.obo FP /^id: EDAM:0001234\n/ FC = 239 FP 26 /^id: / FP 23 /^def: .*multiple / FP 2 /^def: .*multiple\)/ FP 2 /^def: Multiple / // ID edamhasinput-ex AP edamhasinput CL sequence IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamhasinput.obo FP /^id: EDAM:0000346\n/ FP 30 /^id: / FP 30 /^namespace: operation/ FP 2 /^relationship: has_input EDAM:0000849 \! Sequence record/ FP 4 /^relationship: has_input EDAM:0000863 \! Sequence alignment/ FC = 334 // ID edamhasoutput-ex AP edamhasoutput CL sequence IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamhasoutput.obo FP /^id: EDAM:0000448\n/ FP 48 /^id: / FP 48 /^namespace: operation/ FP 1 /^relationship: has_output EDAM:0000849 \! Sequence record/ FP 5 /^relationship: has_output EDAM:0001298 \! Sequence features \(motifs\)/ FP 1 /^relationship: has_output EDAM:0000857 \! Database hits \(sequence\)/ FP 3 /^relationship: has_output EDAM:0000863 \! Sequence alignment/ FC = 537 // ID edamisformat-ex AP edamisformat CL sequence IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamisformat.obo FC = 171 FP /^id: EDAM:0001921\n/ FP 19 /^id: / FP 19 /^namespace: format/ FP 1 /^relationship: is_format_of EDAM:0000863 \! Sequence alignment\n/ FP 1 /^relationship: is_format_of EDAM:0000924 \! Sequence trace\n/ // ID edamisid-ex AP edamisid CL sequence IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamisid.obo FC = 153 FP /^id: EDAM:0001094\n/ FP 15 /^id: / FP 14 /^namespace: identifier/ FP 7 /^relationship: is_identifier_of EDAM:0000849 \! Sequence record\n/ // ID edamname-ex AP edamname CL "*sequence_set*" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamname.obo FP /^id: EDAM:0001234\n/ FP 6 /^id: / FP 6 /^name: Sequence set/ FP 1 /^name: .*Sequence set$/ FC = 53 // ID edamname-ex2 AP edamname CL "*sequence_set*" -subclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edamname.obo FC = 227 FP /^id: EDAM:0001234\n/ FP 24 /^id: / FP 6 /^name: Sequence set/ // ID edialign-ex AP edialign IN ../../data/vtest.seq IN IN FI vtest.fasta FC = 12 FP /ldtapC-LFSDGSPQKAAYVLWDQTILQQDITPLPSHethsaqkgELLAliCglraAKPW\n/ FP /pghqkghsaeargnrmADQAARKAAITETPDTSTLL-----\n/ FP /rpgl-CqVFADATPTGWGLVMGHQRMRGTFSAPLPIHta------ELLAa-Cf---ARSR\n/ FP /SGANIIg-----------------------------------------------------\n/ FP /----------------TDNSGRTSLYADSPSVPSHLpdrvh\n/ FP 3 /^>/ FI vtest.edialign FC = 76 FP 4 /^HTL2 +/ FP /HTL2 +1 ldtapC-LFS DGSPQKAAYV LWDQTILQQD ITPLPSHeth saqkgELLAl \n/ FP / +0000000999 9999999999 9999999999 9999999000 0000000000 \n/ FP / +0000000000 0077777777 7000000000 0000000000 0000000000 \n/ FP / +0000000000 0000000000 0000000000 0000001111 1111111111 \n/ FP / +1111110000 0 \n/ FP /\n/ FP /\n/ FP /\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID einverted-ex AP einverted ## ## timeout more than 60 seconds ## or we may need a quicker example ## TI 500 CL tembl:d00596 IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI d00596.fasta FC = 26 FP 8 /^>/ FP /^>D00596_12246_12296\nctcc.*ccatgcc\n>D00596_13886_13938\nggtatgg.*aggag/ FI d00596.inv FP /Score 236: 108/130 \( 83%\) matches, 0 gaps/ // ID embossdata-ex UC Display the directories searched for EMBOSS data files: AP embossdata IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /Exists\n/ // ID embossdata-ex2 UC Display the names of data files in all of the possible data directories: UC This is run on a small test system and so the results will probably UC be different when you run this. AP embossdata CL -showall IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^DIRECTORY: .*data[\/\\]?\n/ FP /^DIRECTORY: .*data[\/\\]CODONS[\/\\]?\n/ FP /^\s*EBLOSUM62\s*\n/ FP /^\s*Eyeast\.cut\s*\n/ // ID embossdata-exfile UC Display the directories which contain a particular EMBOSS data file: AP embossdata CL EPAM60 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^File \.[\/\\]EPAM60/ FP /^File \.embossdata[\/\\]EPAM60/ // ID embossdata-exfetch UC Make a copy of an EMBOSS data file in the current directory: AP embossdata CL -fetch Epepcoil.dat FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^File '.*data[\/\\]Epepcoil\.dat' has been copied successfully\.\n/ FI Epepcoil.dat FZ = 1445 FP /\A# Input data for PEPCOIL *\n/ // ID embossversion-ex AP embossversion FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^[1-9]\.\d+\.\d+\.\d+\n/ // ID emowse-ex AP emowse IN tsw:* IN ../../data/test.mowse IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 12s1_arath.emowse FC = 177 FP /^1 UBR5_RAT/ FP /1 : UBR5_RAT\s+1\.233e\+0+6 103949\.9 0\.750/ // ID emma-ex RQ clustalw AP emma IN ../../data/globins.fasta IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## ## stdout is written by clustalw, invoked by emma ## ## exact output file contents depend on the clustalw version ## this is for clustalw 1.82, built from ## ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.82.UNIX.tar.gz ## file size 606683 date 'Feb 6 2001' ## FI stdout FC > 50 FP /^Sequences \(1:2\) Aligned\. Score: 83\n/ FP /^Alignment Score 4164\n/ FP /^GCG-Alignment file created +\S+\Z/ FI hbb_human.aln FZ = 1262 FP /^--------VHLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST\n/ FI hbb_human.dnd FZ = 186 FP /^HBB_HUMAN:0\.08080,\nHBB_HORSE:0\.08359\)\n/ // ID emma-dna RQ clustalw AP emma IN ../../data/tropomyosin.fasta IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## ## stdout is written by clustalw, invoked by emma ## ## exact output file contents depend on the clustalw version ## this is for clustalw 1.82, built from ## ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/clustalw1.82.UNIX.tar.gz ## file size 606683 date 'Feb 6 2001' ## FI stdout FC = 120 FP /^Sequences \(1:2\) Aligned\. Score: 59\n/ FP /^Alignment Score 127498\n/ FP /^GCG-Alignment file created +\S+\Z/ FI bf056441.aln FC = 299 FP /^TTC----TTACAAGAGAAGAGAA--AGACCCAC-----GGAGCTCCAG--AGTTTCTGTT\n/ FI bf056441.dnd FC = 34 FP /^AF186110:0.00114,\n/ FP /AF362887:0.07397\)\n/ FP 11 /^\(\n/ // ID entret-ex AP entret CL tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.entret FZ = 3331 FP /^FT CDS 57\.\.458\n/ FP /^\/\/\Z/ // ID seq-textauto-acedb AP entret CL -auto ../../data/dna.acedb test.out FI test.out FZ = 117 FC = 4 FP /DNA : "ACEDB"\n/ FP /GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT/ // ID seq-text-acedb AP entret CL -auto ../../data/dna.acedb -sf acedb test.out FI test.out FZ = 117 FC = 4 FP /DNA : "ACEDB"\n/ FP /GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT/ // ID seq-textauto-codata AP entret CL -auto ../../data/dna.codata test.out FI test.out FC = 10 FP /^ENTRY CODATA *\n/ FP /^ 91 G T A C G T A C G T\n/ // ID seq-text-codata AP entret CL -auto ../../data/dna.codata -sf codata test.out FI test.out FZ = 423 FC = 10 FP /^ENTRY CODATA *\n/ FP /^ 91 G T A C G T A C G T\n/ // ID seq-textauto-embl AP entret CL -auto ../../data/dna.embl test.out FI test.out FZ = 487 FC = 18 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt +100\n/ // ID seq-text-experiment AP entret CL -auto ../../data/xb63c7.s1.exp -sf experiment test.out FI test.out FZ = 2317 FC = 51 FP /^ID xb63c7\.s1\n/ FP /^ TAATTTTCAA AAG-CCA-G\n/ FP /^SR 440\n/ // ID seq-textauto-experiment AP entret CL -auto ../../data/xb63c7.s1.exp test.out FI test.out FZ = 2317 FC = 51 FP /^ID xb63c7\.s1\n/ FP /^ TAATTTTCAA AAG-CCA-G\n/ FP /^SR 440\n/ // ID seq-text-embl AP entret CL -auto ../../data/dna.embl -sf embl test.out FI test.out FZ = 487 FC = 18 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt +100\n/ // ID seq-textauto-fasta AP entret CL -auto ../../data/dna.fasta test.out FI test.out FZ = 143 FC = 4 FP /^>FASTA F10002 FASTA FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-text-fasta AP entret CL -auto ../../data/dna.fasta -sf fasta test.out FI test.out FZ = 143 FC = 4 FP /^>FASTA F10002 FASTA FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-textauto-gcg AP entret CL -auto ../../data/dna.gcg test.out FI test.out FZ = 362 FC = 14 FP /^GCG Length: 100 Type: N Check: 6856 \.\.\n/ FP /^ 1 ACGTAC\gnl\|N10002\|NCBI NCBI FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-text-ncbi AP entret CL -auto ../../data/dna.ncbi -sf ncbi test.out FI test.out FZ = 145 FC = 4 FP /^>gnl\|N10002\|NCBI NCBI FORMAT DNA SEQUENCE\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-textauto-nbrf AP entret CL -auto ../../data/prot.nbrf test.out FI test.out FZ = 132 FC = 6 FP /^>P1;pir\n/ FP /^ ABCDEFGHIK LMNPQRSTVW XYZACGTU\.-\n/ // ID seq-text-nbrf AP entret CL -auto ../../data/prot.nbrf -sf nbrf test.out FI test.out FZ = 132 FC = 6 FP /^>P1;pir\n/ FP /^ ABCDEFGHIK LMNPQRSTVW XYZACGTU\.-\n/ // ID seq-textauto-raw AP entret CL -auto ../../data/dna.text test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-text-raw AP entret CL -auto ../../data/dna.text -sf raw test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-textauto-staden AP entret CL -auto ../../data/dna.staden test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-text-staden AP entret CL -auto ../../data/dna.staden -sf staden test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-textauto-strider AP entret CL -auto ../../data/dna.strider test.out FI test.out FZ = 168 FC = 6 FP /^; DNA sequence STRIDER, 100 bases\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-text-strider AP entret CL -auto ../../data/dna.strider -sf strider test.out FI test.out FZ = 168 FC = 6 FP /^; DNA sequence STRIDER, 100 bases\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-textauto-textonly AP entret CL -auto ../../data/dna.text test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-text-textonly AP entret CL -auto ../../data/dna.text -sf textonly test.out FI test.out FZ = 102 FC = 2 FP /^ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC\n/ FP /^GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-textauto-abi AP entret CC Fails ... ABI reading functions use raw file pointer not the buffer CL -auto ../../data/abiview.abi test.out FI test.out FZ = 0 FI stderr FP /Warning: Failed to read text from binary ABI file \.\.[\/\\]\.\.[\/\\]data[\/\\]abiview\.abi/ FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID seq-text-selex AP entret CL -auto ../../data/test.selex -sf selex test.out FI test.out FZ = 610 FC = 20 FP /^#=ID r17\n/ FP /^lig2 AUGGAUGCGCACC AUCA GGGCGUAUCUAU\n/ // ID seq-textmultiauto-acedb AP entret CL -auto ../../data/dna.m-acedb test.out FI test.out FZ = 420 FC = 15 FP /^DNA : "ACEDBM1"\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-textmulti-acedb AP entret CL -auto ../../data/dna.m-acedb -sf acedb test.out FI test.out FZ = 420 FC = 15 FP /^DNA : "ACEDBM1"\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-textmultiauto-codata AP entret CL -auto ../../data/dna.m-codata test.out FI test.out FZ = 1416 FC = 30 FP /^ENTRY CODATAM1 +\n/ FP /^ 91 G T A C G T A C G T A C G T A C G T A C G T A C G T A C G T\n/ // ID seq-textmulti-codata AP entret CL -auto ../../data/dna.m-codata -sf codata test.out FI test.out FZ = 1416 FC = 30 FP /^ENTRY CODATAM1 +\n/ FP /^ 91 G T A C G T A C G T A C G T A C G T A C G T A C G T A C G T\n/ // ID seq-textmultiauto-embl AP entret CL -auto ../../data/dna.m-embl test.out FI test.out FZ = 945 FC = 21 FP 3 /^ID/ FP /^ +CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT +120\n/ // ID seq-textmulti-embl AP entret CL -auto ../../data/dna.m-embl -sf embl test.out FI test.out FZ = 945 FC = 21 FP 3 /^ID/ FP /^ +CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT +120\n/ // ID seq-textmultiauto-fasta AP entret CL -auto ../../data/dna.m-fasta test.out FI test.out FZ = 516 FC = 12 FP 3 /^>/ FP /^CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA\n/ // ID seq-textmulti-fasta AP entret CL -auto ../../data/dna.m-fasta -sf fasta test.out FI test.out FZ = 516 FC = 12 FP 3 /^>/ FP /^CGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA\n/ // ID seq-textmultiauto-msf AP entret CL -auto ../../data/dna.msf test.out FI test.out FZ = 820 FC = 22 FP 3 /^ Name: MSF/ FP /^ MSFM3 ACGTACGTAC GTACGTACGT\n/ // ID seq-textmulti-msf AP entret CL -auto ../../data/dna.msf -sf msf test.out FI test.out FZ = 820 FC = 22 FP 3 /^ Name: MSF/ FP /^ MSFM3 ACGTACGTAC GTACGTACGT\n/ // ID seq-textmultiauto-msf8 AP entret CL -auto ../../data/dna.msf8 test.out FI test.out FZ = 1084 FC = 30 FP 3 /^ Name: fastam/ FP /^fastam3 TACGTACGTA CGTACGTACG T\n/ // ID seq-textmulti-msf8 AP entret CL -auto ../../data/dna.msf8 -sf msf test.out FI test.out FZ = 1084 FC = 30 FP 3 /^ Name: fastam/ FP /^fastam3 TACGTACGTA CGTACGTACG T\n/ // ID seq-textmultiauto-ncbi AP entret CL -auto ../../data/dna.m-ncbi test.out FI test.out FZ = 594 FC = 12 FP 3 /^>/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID seq-textmulti-ncbi AP entret CL -auto ../../data/dna.m-ncbi -sf ncbi test.out FI test.out FZ = 594 FC = 12 FP 3 /^>/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID seq-textmultiauto-phylip AP entret CL -auto ../../data/dna.phylip test.out FI test.out FZ = 495 FC = 12 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID seq-textmulti-phylip AP entret CL -auto ../../data/dna.phylip -sf phylip test.out FI test.out FZ = 495 FC = 12 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID seq-textmultiauto-phylipnon AP entret CL -auto ../../data/dna.phylip3 test.out FI test.out FZ = 492 FC = 10 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID seq-textmulti-phylipnon AP entret CL -auto ../../data/dna.phylip3 -sf phylip test.out FI test.out FZ = 492 FC = 10 FP 3 /^MSFM/ FP /^ ACGTACGTTG CAACGTACGT\n/ // ID seq-textmultiauto-strider AP entret CL -auto ../../data/dna.m-strider test.out FI test.out FZ = 648 FC = 21 FP 3 /^; DNA sequence STRIDERM/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID seq-textmulti-strider AP entret CL -auto ../../data/dna.m-strider -sf strider test.out FI test.out FZ = 648 FC = 21 FP 3 /^; DNA sequence STRIDERM/ FP /^GGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTTAACCGGTT\n/ // ID seq-textauto-nonewline AP entret CL -auto ../../data/dna.nonewline test.out FI test.out FZ = 51 FC = 2 FP /^>\n/ FP /^aaaaccccggggttttaaaaccccggggttttaaccggttshshshsh$/ // ID seq-textauto-empty AP entret CL -auto stdin test.out ER 1 FI stderr FZ = 109 FP /Error: Unable to read sequence 'stdin'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID epestfind-ex AP epestfind CL -graph cps -invalid IN ../../data/exu2_drops.embl IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created epestfind\.ps\n/ FI exu2_drops.epestfind FZ = 3194 FP /238 KMVYEMALQLIESESTESPESFESPESSESSEAEVK 273/ FI epestfind.ps FC = 523 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID eprimer3-ex RQ primer3 AP eprimer3 CL tembl:x65921 x65921.eprimer3 -explain FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.eprimer3 FZ = 1427 FP /^\n/ FP /^# considered 16422\n/ FP /^# GC content failed 156\n/ FP /^# ok 2960\n/ FP /^# considered 16330\n/ FP /^# ok 2902\n/ FP /^# considered 2652\n/ FP /^# unacceptable product size 2444\n/ FP /^# ok 186\n/ FP /^ 1 PRODUCT SIZE: 202\n/ FP /^ FORWARD PRIMER 801 20 59\.72 60\.00 CCCAGGAGCTACACACCTTC\n/ FP /^ REVERSE PRIMER 983 20 59\.81 55\.00 GGAGCACGACTTGATCTTCC\n/ FP 5 /PRODUCT SIZE: +[0-9]+/ // ID eprimer32-ex RQ primer32 AP eprimer32 CL tembl:x65921 x65921.eprimer32 -explain FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.eprimer32 FZ = 1364 FP /^\n/ FP /^# considered 18855\n/ FP /^# GC content failed 156\n/ FP /^# ok 5759\n/ FP /^# considered 18706\n/ FP /^# ok 5739\n/ FP /^# considered 4135\n/ FP /^# unacceptable product size 3770\n/ FP /^# ok 336\n/ FP /^ FORWARD PRIMER 826 20 60\.04 70\.00 GACCGGCCAGGAAACGGTCG\n/ FP /^ REVERSE PRIMER 380 20 59\.84 65\.00 CCGCGCGGTTCCCTGCTATT\n/ FP 5 /^ FORWARD PRIMER\s+\d+/ FP 5 /^ REVERSE PRIMER\s+\d+/ // ID equicktandem-ex UC The input sequence is the human herpesvirus tandem repeat. AP equicktandem CL -noorigfile IN tembl:L46634 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.qtan FC = 25 FP /^ +191 935 [+] 339 6 124\n/ // ID est2genome-ex TI 200 AP est2genome IN tembl:h45989 IN tembl:z69719 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI h45989.est2genome FZ = 3050 FP /Note .* forward est and forward genome, .* imply REVERSED GENE/ FP /^Exon 163 91\.8 25685 25874 Z69719 1 193 H45989/ // ID est2genome-pax TI 200 AP est2genome IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-align TI 200 AP est2genome CL -align IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 8086 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ FP /^HSA1280 9567 ttgaggccctggagaaaggtgat\.\.\.\.\.ttcagagtttgagagaacccat 10116\n/ FP /^ [|]+>>>>> 515 >>>>>[|]+\n/ FP /^ pax6 1082 ttgaggccctggagaaag\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.agtttgagagaacccat 1116\n/ // ID est2genome-align-linear TI 200 AP est2genome CL -align -space 2 IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 8086 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ FP /^HSA1280 9567 ttgaggccctggagaaaggtgat\.\.\.\.\.ttcagagtttgagagaacccat 10116\n/ FP /^ [|]+>>>>> 515 >>>>>[|]+\n/ FP /^ pax6 1082 ttgaggccctggagaaag\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.agtttgagagaacccat 1116\n/ // ID est2genome-align-best TI 200 AP est2genome CL -align -best IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 8086 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-both TI 200 AP est2genome CL -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-both2 TI 200 AP est2genome CL -sreverse -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2104 FP /Note .* forward est and forward genome, .* imply REVERSED GENE/ FP /^Exon 129 99\.2 20744 20874 HSA1280 1141 1271 pax6/ CC Note the nosplice version of this test does not have "REVERSED GENE" CC This is only because with no splice consensus penalty the same score CC is found in both directions and the forward gene is the one reported // ID est2genome-mode-forward TI 200 AP est2genome CL -mode forward IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2050 FP /Note requested forward est and forward genome/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-reverse TI 200 AP est2genome CL -mode reverse -srev1 IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2051 FP /Note requested reversed est and forward genome/ FP /^Exon 129 99\.2 1380 1510 HSA1280 428 558 pax6/ // ID est2genome-mode-reverse2 TI 200 AP est2genome CL -mode reverse IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 47 FP /Note requested reversed est and forward genome/ FP 0 /^Exon/ // ID est2genome-nosplice-both TI 200 AP est2genome CL -nousesplice -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 124 99\.2 1380 1505 HSA1280 428 553 pax6/ // ID est2genome-nosplice-both2 TI 200 AP est2genome CL -sreverse -nousesplice -mode both IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2103 FP /Note .* forward est and forward genome, .* imply forward gene/ FP /^Exon 132 99\.3 20741 20874 HSA1280 1138 1271 pax6/ CC Note the mode version of this test has "imply REVERSED GENE" CC This is only because with no splice consensus penalty the same score CC is found in both directions and the forward gene is the one reported // ID est2genome-nosplice-forward TI 200 AP est2genome CL -nousesplice -mode forward IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2050 FP /Note requested forward est and forward genome/ FP /^Exon 124 99\.2 1380 1505 HSA1280 428 553 pax6/ // ID est2genome-nosplice-reverse TI 200 AP est2genome CL -nousesplice -mode reverse -srev1 IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 2051 FP /Note requested reversed est and forward genome/ FP /^Exon 124 99\.2 1380 1505 HSA1280 428 553 pax6/ // ID est2genome-nosplice-reverse2 TI 200 AP est2genome CL -nousesplice -mode reverse IN ../../data/pax6_cdna.fasta IN ../../data/z83307.seq IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pax6.est2genome FZ = 47 FP /Note requested reversed est and forward genome/ FP 0 /^Exon/ // ID etandem-ex UC The input sequence is the human herpesvirus tandem repeat. AP etandem CL -noorigfile IN tembl:L46634 IN 6 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.tan FC = 33 FP /^# HitCount: 5\n/ FP /^ 793 936 [+] 120 6 24 93\.8 acccta \n/ FP /^ 793 936 [+] 120 6 24 93\.8 acccta \n/ FP /^ 432 485 [+] 38 6 9 90\.7 ccctaa \n/ FP /^ 494 529 [+] 26 6 6 94\.4 ccctaa \n/ FP /^ 568 597 [+] 24 6 5 100\.0 aaccct \n/ // ID extractalign-ex UC Extract the region from position 10 to 20: AP extractalign CL ../../data/dna.msf result.seq -regions "11-30" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result.seq FZ = 84 FP /^GTACGTACGT----ACGTAC\n/ FP 3 /^>/ // ID extractfeat-ex UC To write out the exons of a sequence: AP extractfeat CL tembl:x65921 -type exon IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.fasta FZ = 743 FP 5 /^>X65921_/ FP /^>X65921_951_1095 \[exon\] H\.sapiens fau 1 gene\n/ FP /^gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag\n/ // ID extractfeat-ex2 UC To write out the exons with 10 extra bases at the start and end so that you can inspect the splice sites: AP extractfeat CL tembl:x65921 -type exon -before 10 -after 10 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.fasta FZ = 844 FP 5 /^>X65921_/ FP /^>X65921_951_1095 \[exon\] H\.sapiens fau 1 gene\n/ FP /^cccactacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagact\n/ FP /^cctaaggtgagtgaga\n/ // ID extractfeat-ex3 UC To write out the 10 bases around the start of all 'exon' features in the tembl database: AP extractfeat CL "tembl:*" -type exon -before 5 -after -5 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI h45989.fasta FZ = 85782 FP 5 /^>X65921_/ FP 811 /^>/ FP /^>X65921_951_1095 \[exon\] H\.sapiens fau 1 gene\n/ // ID extractfeat-ex4 UC To extract the CDS region with the exons joined into one sequence: AP extractfeat CL tembl:x65921 -type CDS -join IN FI stderr FC = 2 FI x65921.fasta FZ = 453 FP /^>X65921_782_1912 \[CDS\] H\.sapiens fau 1 gene\n/ // # The example has phosphorylation, we only have features that say # PHOSPHORYLATION (BY RK) (BY SIMILARITY). ID extractfeat-ex5 UC To write out the 7 residues around all phosphorylated serine residues ## in the tsw database AP extractfeat CL "tsw:*" -type MOD_RES -value "phosphoserine*" -before 3 -after -4 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 12s1_arath.fasta FZ = 2271 FP 17 /^>/ FP 17 /\[protein_modification_categorized_by_chemical_process\]/ FP /^>OPSD_HUMAN_343_343 \[protein_modification_categorized_by_chemical_process\] Rhodopsin \(Opsin-2\)\n/ FP /^TETSQVA\n/ FP /^>PAXI_HUMAN_109_109 \[protein_modification_categorized_by_chemical_process\] Paxillin\n/ FP /^SPCSRVG\n/ // # use database entry in example ID extractseq-ex UC Extract the region from position 10 to 20: AP extractseq CL tembl:x65923 result.seq -regions "10-20" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result.seq FZ = 48 FP /^ctcgactccat\n/ // # use database entry in example ID extractseq-ex2 UC Extract the regions 10 to 20, 30 to 45, 533 to 537: AP extractseq CL tembl:x65921 result2.seq -regions "10-20 30-45 533-537" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI result2.seq FZ = 71 FP /^tccctctcgatacactcgggacaagttagggc\n/ // # use database entry in example ID extractseq-ex3 UC Extract the regions 782-856, 951-1095, 1557-1612 and 1787-1912: AP extractseq CL tembl:x65921 -reg "782..856,951..1095,1557..1612,1787..1912" stdout FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 8 FZ = 447 FP /^atgcagctctttg[^\n]+ccaggaaacg/ FP /^cccacctttggcaagaagaagggccccaatgccaactcttaa\n/ // ID extractseq-ex4 UC Extract the regions 782-856, 951-1095, 1557-1612 and 1787-1912 all to separate output sequences: AP extractseq CL tembl:x65921 -reg "782..856,951..1095,1557..1612,1787..1912" stdout -separate FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 13 FZ = 564 FP /^>X65921_782_856/ FP /atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg\ngtcgcccagatcaag/ FP /gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag/ FP /^tcttaa\n/ // ID featcopy-ex AP featcopy IN ../../data/paamir.gff3 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.gff FC = 15 FP /X13776\tEMBL\tdatabank_entry\t1\t2167\t\.\t\+\t\.\tID=X13776\.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type=genomic DNA;db_xref=taxon:287\n/ FP /X13776\tEMBL\tsequence_feature\t1\t1\t\.\t\+\t.\tID=X13776.8;note=last base of an XhoI site\n/ // ID feattext-ex AP feattext IN ../../data/paamir.gff3 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.feattext FC = 15 FP /X13776\tEMBL\tdatabank_entry\t1\t2167\t\.\t\+\t\.\tID=X13776\.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type=genomic DNA;db_xref=taxon:287\n/ FP /X13776\tEMBL\tsequence_feature\t1\t1\t\.\t\+\t.\tID=X13776.8;note=last base of an XhoI site\n/ // ID featreport-ex AP featreport IN ../../data/paamir.fasta IN ../../data/paamir.gff IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FC = 15 FP /\A##gff-version 3\n/ FP 10 /^PAAMIR\tEMBL\t/ // ID findkm-ex AP findkm CL -graph cps IN ../../data/enztest.dat IN FI stdout FZ = 18 FP /^Created findkm\.ps\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI enztest.findkm FP /^Vmax = 99\.70, Km = 4\.8946\d+\n/ FI findkm.ps FC = 547 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID freak-ex AP freak CL tembl:x65923 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.freak FZ = 9828 FP /^24 0\.733333\n/ FP /^36 0\.600000\n/ FP /^489 0\.266667\Z/ // ID fuzznuc-ex AP fuzznuc IN tembl:L46634 IN AAGCTT IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.fuzznuc FC = 35 FP /^# HitCount: 2\n/ FP /^ 1 6 [+] pattern: AAGCTT . aagctt\n/ FP /^ 1267 1272 [+] pattern: AAGCTT . aagctt\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 2\n/ // ID fuzznuc-rev AP fuzznuc CL -complement IN asis::GATAAAAAAAAAAAAAAAAAAAAAAAAGATAAAATATCGATA IN GATA IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FC = 39 FP /^# HitCount: 4\n/ FP /^ 1 4 [+] pattern: GATA . GATA\n/ FP /^ 28 31 [+] pattern: GATA . GATA\n/ FP /^ 39 42 [+] pattern: GATA . GATA\n/ FP /^ 35 38 [-] pattern: GATA . GATA\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 4\n/ // ID fuzznuc-ex2 AP fuzznuc IN tembl:L46634 IN @../../data/nucseq.pat IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.fuzznuc FC = 35 FP /^# HitCount: 2\n/ FP /^ 429 448 [+] targetseq: cg\(2\)c\(3\)taaccctagc\(3\)ta \. cggccctaaccctagcccta\n/ FP /^ 491 510 [+] targetseq: cg\(2\)c\(3\)taaccctagc\(3\)ta \. cggccctaaccctagcccta\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 2\n/ // ID fuzznuc-ex3 AP fuzznuc CL -pname test IN tembl:L46634 IN @../../data/nucsimple.pat IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.fuzznuc FC = 48 FP /^# HitCount: 13\n/ FP /^ 429 438 [+] test1: cg\(2\)c\(3\)taac \. cggccctaac\n/ FP /^ 801 810 [+] test2: cctagc\(3\)ta \. cctagcccta\n/ FP 8 /^ +\d+ +\d+ [+-] test1: +/ FP 5 /^ +\d+ +\d+ [+-] test2: +/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 13\n/ // ID fuzznuc-ex4 AP fuzznuc IN tembl:L46634 IN @../../data/nuc.pat IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.fuzznuc FC = 54 FP /^# HitCount: 19\n/ FP /^ 429 448 [+] pat1: cggccctaaccctagcccta \. cggccctaaccctagcccta\n/ FP /^ 491 510 [+] pat2: cg\(2\)c\(3\)taaccctagc\(3\)ta \. cggccctaaccctagcccta\n/ FP /^ 535 554 [+] pat2: cg\(2\)c\(3\)taaccctagc\(3\)ta 1 cggccctaaccctaacccta\n/ FP /^ 753 764 [+] pat3: cggc\(2,4\)taac\(2,5\) . cggccctaaccc\n/ FP 8 /^\s+\d+\s+\d+\s+[+-]\s+pat3:/ FP 9 /^\s+\d+\s+\d+\s+[+-]\s+pat2:/ FP 7 /^\s+\d+\s+\d+\s+[+-]\s+pat2:\s\S+\s+1\s+/ FP 2 /^\s+\d+\s+\d+\s+[+-]\s+pat2:\s\S+\s+\.\s+/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 19\n/ // ID fuzzpro-ex AP fuzzpro IN tsw:* IN [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 12s1_arath.fuzzpro FC = 137 FP 8 /^# HitCount: 1\n/ FP 8 /^# HitCount: [1-9]\d*/ FP /^ 53 63 pattern: \[FY\]-\[LIV\]-G-\[DE\]-E-A-Q-x-\[RKQ\]\(2\)-G . YVGDEAQSKRG\n/ FP 4 /^ 53 63 pattern: \[FY\]-\[LIV\]-G-\[DE\]-E-A-Q-x-\[RKQ\]\(2\)-G . YVGDEAQSKRG\n/ FP 4 /^ 55 65 pattern: \[FY\]-\[LIV\]-G-\[DE\]-E-A-Q-x-\[RKQ\]\(2\)-G . YVGDEAQSKRG\n/ FP /^# Reported_sequences: 8\n/ FP /^# Reported_hitcount: 8\n/ // ID fuzztran-ex AP fuzztran CL -opt IN tembl:Z46957 IN RA IN f IN IN FI stderr FC = 31 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI z46957.fuzztran FC = 44 FP /^# HitCount: 9\n/ FP /^ 919 924 [+] 2 pattern: RA . 1 307 308 RA \n/ FP /^ 752 757 [+] 2 pattern: RA . 2 251 252 RA \n/ FP /^ 72 77 [+] 2 pattern: RA . 3 24 25 RA \n/ FP 6 /^.* 1 +\d+ +\d+ RA +\n/ FP 2 /^.* 2 +\d+ +\d+ RA +\n/ FP 1 /^.* 3 +\d+ +\d+ RA +\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 9\n/ // ID seq-infeat-embl TI 120 AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft embl::test.out -auto FI test.out FZ = 78245 ## one_of to order FP /^FT polyA_signal order\(368\.\.373,459\.\.464\)\n/ ## group to order FP /^FT misc_feature order\(226\.\.288,688\.\.754\)\n/ ## Internal quotes FP /^FT ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^FT misc_feature 135\.\.1292\n/ ## Case fix for tag /Translation FP /^FT \/translation="MSANSL/ ## Case fix for type Cds FP /^FT CDS 1289\.\.1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID seq-outfeat-gff AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft gff::test.out -auto FI test.out FC = 648 FZ = 57935 ## Internal quotes FP /\tCDS\t1289\t1879\t\.\t\+\t0\tID=AB036666\.87;.* of "amiE" / // ID seq-outfeat-gb AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.emft gb::test.out -auto FI test.out FZ = 75593 ## Internal quotes FP /^ ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^ misc_feature 135\.\.1292\n/ ## Case fix for tag /Translation FP /^ \/translation="MSANSL/ ## Case fix for type Cds FP /^ CDS 1289\.\.1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID seq-infeat-genbank AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.gbft em::test.out -auto FI test.out FZ = 78387 ## Internal quotes FP /^FT ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^FT misc_feature 135\.\.1292\n/ ## Case fix for tag /Translation FP /^FT \/translation="MSANSL/ ## Case fix for type Cds FP /^FT CDS 1289\.\.1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID seq-infeat-genbank-toembl AP seqret CL -feat ../../data/feat.fasta -ufo ../../data/feat.gbft em::test.out -auto FI test.out FZ = 78387 ## Internal quotes FP /^FT ""amiE"" gene"\n/ ## Bad features type (CODS) to misc_feature FP /^FT misc_feature 135\.\.1292\n/ ## Case fix for tag /Translation FP /^FT \/translation="MSANSL/ ## Case fix for type Cds FP /^FT CDS 1289\.\.1879\n/ ## Cleanup of extra white space 'positive regulator' FP /\/note="aliphatic amidase regulator, positive regulator of\n/ // ID seq-infeat-pir AP seqret CL -feat ../../data/featprot.fasta -ufo pir::../../data/feat.pir sw::test.out -auto FI test.out FZ = 5120 ## active site two locations with copied annotation (note and comment) FP /^FT ACT_SITE 38 38 Cys, His \(status experimental\)\.\n/ FP /^FT ACT_SITE 90 90 Cys, His \(status experimental\)\.\n/ // ID seq-infeatauto-pir AP seqret CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir sw::test.out -auto FI test.out FZ = 5120 ## active site two locations with copied annotation (note and comment) FP /^FT ACT_SITE 38 38 Cys, His \(status experimental\)\.\n/ FP /^FT ACT_SITE 90 90 Cys, His \(status experimental\)\.\n/ // ID seq-infeat-nbrf AP seqret CL -feat ../../data/featprot.fasta -ufo nbrf::../../data/feat.pir sw::test.out -auto FI test.out FZ = 5120 ## active site two locations with copied annotation (note and comment) FP /^FT ACT_SITE 38 38 Cys, His \(status experimental\)\.\n/ FP /^FT ACT_SITE 90 90 Cys, His \(status experimental\)\.\n/ // ID seq-infeat-pir-togff AP seqret CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir gff::test.out -auto FI test.out FC = 67 FZ = 5240 ## active site two locations with copied annotation (note and comment) FP /^OPSD_HUMAN\tPIR\tactive_site_residue\t38\t90\t\.\t\+\t\.\tID=OPSD_HUMAN\.24;note=Cys%2C His;comment=status experimental\n/ FP /^OPSD_HUMAN\tPIR\tactive_site_residue\t90\t90\t\.\t\+\t\.\tParent=OPSD_HUMAN.24\n/ // ID seq-infeat-pir-topir AP seqret CL -feat ../../data/featprot.fasta -ufo ../../data/feat.pir pir::test.out -auto FI test.out FZ = 1756 ## active site two locations with copied annotation (note and comment) FP /^F;38,90\/Active site: Cys, His #status experimental\n/ // ID seq-infeat-refseqp AP seqret CL -feat ../../data/protein.refseqp sw::test.out -auto FI test.out FZ = 2042 ## active site two locations with copied annotation (note and comment) FP /^FT SIGNAL 1 21 ifn-beta. 2410.\n/ FP /^FT REGION 97 97 other. N-glycosylation site. CDD:28979.\n/ // ID seq-infeat-swiss AP seqret CL -feat tsw:laci_ecoli sw::test.out -auto FI test.out FZ = 14190 FP /^FT DNA_BIND 6 25 H-T-H motif\.\n/ FP /^FT HELIX 74 89\n/ // ID seq-infeat-swiss-topir AP seqret CL -feat tsw:laci_ecoli pir::test.out -auto FI test.out FZ = 1846 FP /^F;6-25\/Binding site: H-T-H motif, DNA_contact\n/ FP /^F;74-89\/Region: alpha_helix\n/ // ID seq-infeat-swiss-togff AP seqret CL -feat tsw:laci_ecoli gff::test.out -auto FI test.out FC = 55 FZ = 3441 FP /^LACI_ECOLI\tSWISSPROT\tDNA_contact\t6\t25\t\.\t\+\t\.\tID=LACI_ECOLI\.3;note=H-T-H motif\n/ FP /^LACI_ECOLI\tSWISSPROT\talpha_helix\t74\t89\t\.\t\+\t\.\tID=LACI_ECOLI\.14\n/ // ID garnier-ex AP garnier IN tsw:amic_pseae IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amic_pseae.garnier FC = 84 FP /^# Residue totals: H:103 E:102 T: 86 C: 94\n/ FP /RADA\nhelix HHHHHH HHHH H HHHHHH\n/ FP 1 /^# Reported_sequences: 1\n/ FP 1 /^# Reported_hitcount: 113\n/ // ID garnier-range AP garnier CL -sbegin 51 -send 120 IN tsw:amic_pseae IN FI stderr FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FC = 2 FI amic_pseae.garnier FC = 50 FP /^# Residue totals: H: 17 E: 22 T: 21 C: 10\n/ FP /RADA\nhelix HHHHHH HHHH H HHHHHH\n/ FP /^turns T TTT TTT \n/ FP 1 /^# Reported_sequences: 1\n/ FP 1 /^# Reported_hitcount: 25\n/ // ID garnier-short AP garnier IN asis::GSHQERPL IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI asis.garnier FP /^# Residue totals: H: 0 E: 0 T: 2 C: 6\n/ FP /^turns TT\n/ FP /^ coil CCCCCC \n/ // ID geecee-ex AP geecee CL tembl:L46634 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l46634.geecee FZ = 42 FP /^L46634 0\.53\n/ // ID getorf-ex AP getorf CL -minsize 300 IN tembl:v00294 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00294.orf FZ = 876 FP /^>V00294_1 \[735 - 1112\]/ FP /^TGKRAV\n/ FP /^>V00294_2 \[1 - 1110\]/ FP /^RQVSRLESGQ\n/ FP /^>V00294_3 \[465 - 49\]/ // ID godef-ex AP godef CL glycoprotein IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI godef.obo FP /^id: GO:0015572\n/ FC = 734 FP 68 /^id: / FP 54 /^def: .*glycoprotein / FP 10 /^def: .*glycoprotein\./ FP 5 /^def: .*glycoprotein,/ // ID goname-ex AP goname CL glycoprotein IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI goname.obo FP /^id: GO:0009306\n/ FP /^id: GO:0003980\n/ FC = 967 FP 59 /^id: / FP 29 /^def: .*glycoprotein/ FP 37 /^name: .*glycoprotein/ FP 113 /^synonym: .*glycoprotein/ // ID helixturnhelix-ex AP helixturnhelix IN tsw:laci_ecoli IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.hth FP /^[(]1[)] Score 2160\.000 length 22 at residues 4->25\n/ FP /^ Standard_deviations: 6\.54\n/ // ID hmoment-ex AP hmoment CL tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hbb_human.hmoment FZ = 1494 FP /^Window: 10 Angle: 100 Max uH: 0\.714\n/ FP /^138\s+0\.299\Z/ // ID iep-ex AP iep CL tsw:laci_ecoli IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.iep FZ = 761 FP /^Isoelectric Point = 6\.8820\n/ FP /^ 7\.00 43\.59 -0\.41\n/ // ID iep-ex2 AP iep CL tsw:ifna2_human -disulphide 2 -lysinemodified 2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ifna2_human.iep FZ = 762 FP /^Isoelectric Point = 5\.7322\n/ FP /^ 7\.00 27\.65 -2\.35\n/ // ID iep-ifna2-nooptions AP iep CL tsw:ifna2_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ifna2_human.iep FZ = 762 FP /^Isoelectric Point = 6\.7505\n/ FP /^ 7\.00 33\.53 -0\.47\n/ // # change examples to .msf from .seq # ID infoalign-ex AP infoalign CL ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 8 FP /^msf::\S+msf:HBA_HORSE\s+HBA_HORSE\s+141\s+144\s+2\s+3\s+63\s+6\s+72\s+56\.250000\s+0\.830000\s+\n/ // ID infoalign-ex2 UC This example doesn't display the USA of the sequence: AP infoalign CL ../../data/globins.msf -nousa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 8 FP /^HBA_HORSE\s+141\s+144\s+2\s+3\s+63\s+6\s+72\s+56\.250000\s+0\.830000\s+\n/ // ID infoalign-ex3 UC Display only the name and sequence length of a sequence: AP infoalign CL ../../data/globins.msf -only -name -seqlength IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 7 FP /^HBA_HORSE\s+141\n/ // ID infoalign-ex4 UC Display only the name, number of gap characters and differences to the consensus sequence: AP infoalign CL ../../data/globins.msf -only -name -gapcount -diffcount IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 7 FP /^HBA_HORSE\s+3\s+72\n/ // ID infoalign-ex5 UC Display the name and number of gaps within a sequence: AP infoalign CL ../../data/globins.msf -only -name -gaps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 7 FP /^HBA_HORSE\s+2\n/ // ID infoalign-ex6 UC Display information formatted with HTML: AP infoalign CL ../../data/globins.msf -html IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 94 FP /^msf::\.\./\.\./data/globins\.msf:HBA_HORSE<\/td>\n/ FP /^HBA_HORSE<\/td>\n/ // ID infoalign-ex7 UC Use the first sequence as the reference sequence to compare to: AP infoalign CL ../../data/globins.msf -refseq 1 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.infoalign FC = 8 FP /^msf::\S+\s+HBA_HORSE\s+141\s+144\s+2\s+3\s+51\s+18\s+72\s+64\.583336\s+0\.830000\s+\n/ // ID infoalign-ex8 AP infoalign CL -auto @../../data/eclac.list -out test.out FI test.out FC = 6 FP /tembl-id:J01636\s+J01636\s+7477\s+7477\s+0\s+0\s+374\s+0\s+7103\s+94\.997[0-9]+\s+1\.0+\s+E.*/ FP /tembl-id:V00296\s+V00296\s+3078\s+3078\s+0\s+0\s+373\s+0\s+2705\s+87\.881[0-9]+\s+1\.0+\s+E.*/ // ID infoalign-ex9 AP infoalign CL -auto tembl:v00296 -out test.out FI test.out FC = 2 FP /tembl-id:V00296\s+V00296\s+3078\s+3078\s+0\s+0\s+3078\s+0\s+0\s+0\.0+\s+1\.0+\s+E.*/ // ID infobase-ex AP infobase IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.infobase FC = 18 FP /A A T adenine\n/ FP /K GT M keto_base\n/ // ID inforesidue-ex AP inforesidue IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.inforesidue FC = 27 FP /A Ala alanine 0.0 71.0788 tiny,small,aliphatic,nonpolar A\n/ FP /Z Glx glutamate/glutamine -0.5 128.6231 polar EQ\n/ // ID infoseq-ex UC Display information on a sequence: AP infoseq CL tembl:x13776 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 304 FP /^tembl-id:X13776\s+tembl\s+X13776\s+X13776\s+N\s+2167\s+66\.54\s+Pseudomonas/ // ID infoseq-ex2 UC Don't display the USA of a sequence: AP infoseq CL tembl:x13776 -nousa FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 254 FP /^tembl\s+X13776\s+X13776\s+N\s+2167\s+66\.54\s+Pseudomonas/ // ID infoseq-ex3 UC Display only the name and length of a sequence: AP infoseq CL tembl:x13776 -only -name -length FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 46 FP /^X13776\s+2167\s+\n/ // ID infoseq-ex4 UC Display only the description of a sequence: AP infoseq CL tembl:x13776 -only -desc FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 88 FP /^Pseudomonas aeruginosa .* regulation\n/ // ID infoseq-ex5 UC Display the type of a sequence: AP infoseq CL tembl:x13776 -only -type FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 12 FP /^Type\s+\nN\s+\n/ // ID infoseq-ex6 UC Display information formatted with HTML: AP infoseq CL tembl:x13776 -html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 432 FP /^tembl-id:X13776temblX13776X13776N216766\.54Pseudomonas .* regulation\n/ // ID isochore-ex AP isochore CL tembl:AF129756 -graph cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI af129756.iso FZ = 22819 FP /^5000\s+0\.476\n/ FI isochore.ps FZ > 100 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI stdout FZ = 20 FP /^Created isochore\.ps\n/ // ID jaspextract-keep AP jaspextract DL keep PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/jaspar FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI JASPAR_CNE DI JASPAR_CORE DF MA0070.1.pfm DF MA0071.1.pfm DF MA0072.1.pfm DF MA0073.1.pfm DF MA0074.1.pfm DF MA0075.1.pfm DF MA0076.1.pfm DF MA0077.1.pfm DF MA0078.1.pfm DF MA0079.1.pfm DF matrix_list.txt DI JASPAR_FAM DI JASPAR_PBM DI JASPAR_PBM_HLH DI JASPAR_PBM_HOMEO DI JASPAR_PHYLOFACTS DI JASPAR_POLII DI JASPAR_SPLICE // ID jaspscan-ex AP jaspscan PP EMBOSS_DATA=../jaspextract-keep/ PP export EMBOSS_DATA CL -both IN tembl:m23100 IN IN ma0079.1 IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI m23100.jaspscan FC = 42 FP /^ +117 +126 +[+] +82.143 +MA0079[.]1 +SP1 +9606 +Zinc-coordinating/ FP 12 /^ +\d+ +\d+ +[+]/ FP 6 /^ +\d+ +\d+ +[-]/ // ID jembossctl-ex CC for jemboss installations CC can only be run through tomcat so simply exits here AP jembossctl CL jctl.file FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // # remove the extra 2 prompts from the example ID lindna-ex AP lindna CL -graph cps IN ../../data/data.linp IN IN FI stdout FZ = 18 FP /^Created lindna\.ps\n/ FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI lindna.ps FC = 285 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ## Example should be file1 file2 ID listor-ex UC Write the logical OR of two lists: AP listor CL ../../data/file1 ../../data/file2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 115 FC = 4 FP 4 /^fasta::/ FP 3 /file1/ FP 1 /file2/ // ID listor-ex2 UC Write the logical AND of two lists: AP listor CL ../../data/file1 ../../data/file2 -operator and IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 58 FC = 2 FP 2 /^fasta::/ FP 2 /file1/ FP 0 /file2/ // ID listor-ex3 UC Write the logical XOR of two lists: AP listor CL ../../data/file1 ../../data/file2 -operator xor IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 57 FC = 2 FP 2 /^fasta::/ FP 1 /file1/ FP 1 /file2/ // ID listor-ex4 UC Write the logical NOT of two lists: AP listor CL ../../data/file1 ../../data/file2 -operator not IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI file1.list FZ = 28 FC = 1 FP 1 /^fasta::/ FP 1 /file1/ FP 0 /file2/ FP 1 /file1:one/ // ID makenucseq-ex AP makenucseq IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI makeseq.fasta FC = 300 FP 100 /^>EMBOSS_[0-9][0-9][0-9]/ FP /\A>EMBOSS_001\nggtccgaggggta.*gataaaa\ntaaaatg.*cccta\n/ // ID makenucseq-ex2 UC Providing a codon usage file specifies the sequence composition. UC This Pseudomonas aeruginosa file specifies a high GC content. AP makenucseq IN Epseae.cut IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI makeseq.fasta FC = 300 FP 100 /^>EMBOSS_[0-9][0-9][0-9]/ FP /\A>EMBOSS_001\ngggcgtctg.*gtcaacttc\ngcgcggcag.*gtgcgcg\n/ // ID makeprotseq-ex AP makeprotseq IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI makeseq.fasta FC = 300 FP 100 /^>EMBOSS_[0-9][0-9][0-9]/ FP /\A>EMBOSS_001\nnrvlhpepnprt.*lmmydsqfwcdfe\nwadcc.*gkkvd\n>/ // ID marscan-ex AP marscan IN tembl:u01317 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI u01317.marscan FZ = 1413 FP /\t2242\t2458\t.*start8bp 2451;.*end8bp 2458;.*start16bp 2242;.*end16bp 2257\n/ // ID maskambignuc-ex AP maskambignuc IN ../../data/ambignuc.fasta IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ambignuc.fasta FC = 2 FP /^ANCNGNNNNNNTUNNNancngnnnnnntunnn\n/ // ID maskambigprot-ex AP maskambigprot IN ../../data/ambigprot.fasta IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ambigprot.fasta FC = 2 FP /^AXCDEFGHIXKLMNXPQRSTXVWXYXXaxcdefghixklmnxpqrstxvwxyxX\n/ // ID maskfeat-ex UC Mask out a feature whose type is "repeat_region" from position 2331 to 2356: AP maskfeat CL tembl:ab000360 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ab000360.fasta FZ = 2685 FP /^>AB000360 / FP /^NNNNNNNNNNNNNNNNaaagtcacttctttctacccttttcaatgtgctaatgctctttt\n/ // ID maskfeat-ex2 UC Change to lower-case a feature whose type is "repeat_region" from position 2331 to 2356. Note that '-supper' is used to make the whole sequence upper-case before the lower-case masking: AP maskfeat CL tembl:ab000360 -tolower -supper IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ab000360.fasta FZ = 2685 FP /^>AB000360 / FP /^gtgtgtgtgtgtgtgtAAAGTCACTTCTTTCTACCCTTTTCAATGTGCTAATGCTCTTTT\n/ // ID maskseq-ex UC Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=10-12 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\n/ // ID maskseq-ex2 UC Mask off bases 20 to 30 from a sequence 'prot.fasta' using the character 'x' and write to the new sequence file 'prot2.seq': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=20-30 -mask=x FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\n/ // ID maskseq-ex3 UC Mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY\n/ FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY\n/ // ID maskseq-ex4 UC Change to lower-case the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta': AP maskseq CL ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 -tolower FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prot2.seq FZ = 146 FP /^ACDEFGHIKLMNPQRSTVWyacdEFGHIKLMNPqrstvwyacdefGHIKLMNPQRSTVWY\n/ FP /^ACDEFGHIKLMNPQRSTVWYACDEFGHiklMNPQRSTVWY\n/ // ID matcher-ex AP matcher CL tsw:hba_human tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.matcher FP /^# Identity: +63\/145 \(43\.4%\)/ FP /^# Score: +264\n/ FP /^HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP\n/ FC = 49 // ID matcher-ex2 UC To find the 10 best alignments: AP matcher CL tsw:hba_human tsw:hbb_human -alt 10 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.matcher FP /^# Identity: +63\/145 \(43\.4%\)/ FP /^# Score: +264\n/ FP /^HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP\n/ FC = 275 // ID megamerger-ex TI 300 AP megamerger CL tembl:v00295 tembl:v00296 IN IN IN report FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI report FC = 15 FP /^V00295 overlap starts at 1\n/ FP /^V00296 overlap starts at 3019\n/ FI v00295.merged FZ = 4659 FP /^tgtcaaaaataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaatcc\n/ FP /^ggcttaccggaaaaaaga\n/ // ID merger-ex AP merger IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FZ > 1445 FP /^# Score: 795\.0\n/ FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^X51872 +1 [-]+gtgaatgaa +9\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID msbar-ex UC This asks for 5 mutations, with point mutations as changes (substitutions), and the codon and block mutations ignored. AP msbar IN tembl:j01636 IN 5 IN 4 IN IN IN FI stderr FC = 26 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## ## hard to test - different changes each time FI j01636.fasta FZ = 7679 FP /^>J01636 J01636/ // ID mwcontam-ex AP mwcontam IN ../../data/mw1.dat,../../data/mw2.dat,../../data/mw3.dat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.mwcontam FZ = 15 FP /^67\.000\n/ FP /^415\.000\n/ // ID mwfilter-ex AP mwfilter IN ../../data/molwts.dat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI molwts.mwfilter FZ = 190 FC = 16 FP /^874\.364756\n/ // ID needle-ex AP needle CL tsw:hba_human tsw:hbb_human IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.needle FZ > 1270 FP /^# Score: 292\.5\n/ FP /HBB_HUMAN +1 +MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD +48\n/ FP /HBA_HUMAN +49 +LS-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR +93\n/ // ID needleall-ex AP needleall CL -minscore 40 -stdout -auto CL ../../data/illumina_adapter_primer.fa CL ../../data/test1_illumina.fastq FI stderr FI needleall.error FP /Alignment score \(21.5\) is less than minimum score/ FC = 752 FI stdout FC = 26 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FZ > 1270 FP /^Illumina_DpnII_Gex_PCR_Primer_2.*(41.0)/ // ID newcpgreport-ex AP newcpgreport IN tembl:u68037 IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI u68037.newcpgreport FZ = 540 FP /^FT CpG island 104\.\.509\n/ FP /^FT \/size=406\n/ FP /^FT \/Sum C\+G=269\n/ FP /^FT \/Percent CG=66\.26\n/ FP /^FT \/ObsExp=0\.81\n/ FP /^FT CpG island 596\.\.924\n/ FP /^FT numislands 2\n/ // ID newcpgseek-ex AP newcpgseek IN tembl:u68037 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI u68037.newcpgseek FZ = 277 FP /^with score \> 17 \n/ FP /^\* 96 1032 630 87 66\.1 0\.65\n/ FP /^ 1072 1100 26 3 62\.1 0\.00\n/ FP /^ 1183 1193 26 2 72\.7 2\.00\n/ // # example to use SWISS format (for protein) ID newseq-ex UC Type in a short sequence to the file 'mycc.pep' in SWISSPROT format: AP newseq IN cytoc IN fragment of cytochrome c IN p IN KKKEERADLIAY IN swiss::mycc.pep FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mycc.pep FZ = 167 FP /^ID cytoc Unreviewed; 12 AA\.\n/ FP /^DE fragment of cytochrome c\n/ FP /^SQ SEQUENCE 12 AA; 1464 MW; 6F142FA88DADC40B CRC64;/ // ID nohtml-ex AP nohtml IN ../../data/webfile.html IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI webfile.nohtml FC = 10 FP /^embossdata\n/ FP 5 /^.*\S+.*\n/ // ID noreturn-ex AP noreturn CL ../../data/abc.dat IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI abc.noreturn FZ = 71 FP /carriage return format\nACDEFGHIKLMNPQRSTVWY\n$/ // ID noreturn-topc AP noreturn CL ../../data/abc.dat -system pc IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI abc.noreturn FZ = 73 FP /carriage return format\r\nACDEFGHIKLMNPQRSTVWY\r\n$/ // ID noreturn-tomac AP noreturn CL ../../data/abc.dat -system mac IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI abc.noreturn FZ = 71 FP /carriage return format\rACDEFGHIKLMNPQRSTVWY\r$/ // ID nospace-ex AP nospace IN ../../data/seqspace.txt IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI seqspace.nospace FC = 46 FP /^>X13776\n/ FP /^ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacggga\n/ // ID notab-ex AP notab IN ../../data/tabfile.txt IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI tabfile.notab FC = 9 FP /^a b c d\n/ FP /^ab cd ef g\n/ FP /^abc def ghi j\n/ FP /^abcd efgh ijkl m\n/ FP /^abcde fghij klmno p\n/ FP /^abcdef ghijkl mnopqr s\n/ FP /^abcdefg hijklmn opqrstu v\n/ FP /^abcdefgh ijklmnop\n/ // # change example to use globins.fasta ID notseq-ex UC In this case the excluded sequences (myg_phyca and lgb2_luplu) are not saved to any file: AP notseq IN ../../data/globins.fasta IN myg_phyca,lgb2_luplu IN mydata.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mydata.seq FZ = 926 FP /^>HBA_HUMAN/ FP /^>HBA_HORSE/ FP /^>HBB_HUMAN/ FP /^>HBB_HORSE/ FP /^>GLB5_PETMA/ FP 0 /^>MYG_PHYCA/ FP 0 /^>LGB2_LUPLU/ // ID notseq-ex2 UC Here is an example where the sequences to be excluded are saved to another file: AP notseq CL -junkout hb.seq IN ../../data/globins.fasta IN hb* IN mydata.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mydata.seq FZ = 581 FP 0 /^>HBA_HUMAN/ FP 0 /^>HBA_HORSE/ FP 0 /^>HBB_HUMAN/ FP 0 /^>HBB_HORSE/ FP /^>GLB5_PETMA/ FP /^>MYG_PHYCA/ FP /^>LGB2_LUPLU/ FI hb.seq FP /^>HBB_HUMAN/ // ID nthseq-ex AP nthseq IN @../../data/eclac.list IN 2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.fasta FZ = 1942 FP /^>X51872 X51872\.1 Escherichia coli lacA gene/ // ID nthseqset-ex AP nthseqset CL -osf phylip IN ../../data/globins-all.phy IN 2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins-all.phylip FZ = 1578 FP 1 /^ 7 167\n/ FP /^ FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF\n/ // ID octanol-ex AP octanol IN tsw:opsd_human IN ps FI stdout FZ = 19 FP /^Created octanol\.ps\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI octanol.ps FC = 302 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID octanol-nodiff AP octanol CL -noplotdiff IN tsw:opsd_human IN ps FI stdout FZ = 19 FP /^Created octanol\.ps\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI octanol.ps FC = 262 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID oddcomp-ex UC To search for entries in swissprot with at least 1 SR AND at least 2 RS: AP oddcomp IN tsw:* IN ../../data/oddcomp.comp IN IN out.odd FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI out.odd FP /CNR1B_TAKRU/ FZ = 176 // ID ontocount-ex AP ontocount CL edam:0001234 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^1\n/ // ID ontocount-ex2 AP ontocount CL edam:0001234 -subclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^7\n/ // ID ontoget-ex AP ontoget CL edam:0001234 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0001234.obo FP /^id: EDAM:0001234\n/ FP 1 /^id: / FP 1 /^is_a: EDAM:0000850/ FP 0 /^relationship: / FC = 9 // ID ontogetcommon-ex AP ontogetcommon CL "edam:{0000108,0000110}" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ontogetcommon.obo FP /^id: EDAM:0000197\n/ FP 1 /^id: / FC = 11 // ID ontoget-ex2 AP ontoget CL edam:0000850 -subclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0000850.obo FP /^id: EDAM:0001234\n/ FP 14 /^id: / FP 4 /^is_a: EDAM:0000850/ FP 2 /^is_a: EDAM:0001235/ FP 2 /^relationship: / FC = 127 // ID ontogetdown-ex AP ontogetdown CL edam:0000850 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0000850.obo FP /^id: EDAM:0001234\n/ FP 4 /^id: / FP 4 /^is_a: EDAM:0000850/ FP 2 /^relationship: / FC = 37 // ID ontogetobsolete-ex AP ontogetobsolete CL edam:alignment -subclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0000083.obo FP /^id: EDAM:0000083\n/ FP 1 /^id: / FP 1 /^consider: EDAM:0000182/ FP 1 /^consider: EDAM:0000183/ FP 0 /^relationship: / FC = 11 // ID ontogetroot-ex AP ontogetroot CL edam:0001234 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0001234.obo FP /^id: EDAM:0000006\n/ FP 1 /^id: / FP 0 /^relationship: / FP 0 /^is_a: / FC = 7 // ID ontogetsibs-ex AP ontogetsibs CL edam:0000575 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0000575.obo FP /^id: EDAM:0000575\n/ FP 3 /^id: / FP 2 /^relationship: / FC = 27 // ID ontogetup-ex AP ontogetup CL edam:0001234 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0001234.obo FP /^id: EDAM:0000850\n/ FP /^id: EDAM:0002977\n/ FP 2 /^id: / FP 0 /^relationship: / FC = 18 // ID ontoisobsolete-ex AP ontoisobsolete CL edam:0000181 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^Obsolete\n/ FC = 1 // ID ontoisobsolete-ex2 AP ontoisobsolete CL edam:0000575 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^edam:0000575 OK\n/ FC = 1 // ID ontotext-ex AP ontotext CL edam:0001234 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0001234.ontotext FP /^id: EDAM:0001234\n/ FP 1 /^id: / FP 1 /^is_a: EDAM:0000850/ FP 0 /^relationship: / FC = 9 // ID ontotext-ex2 AP ontotext CL edam:0000850 -subclasses IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 0000850.ontotext FP /^id: EDAM:0001234\n/ FP 14 /^id: / FP 4 /^is_a: EDAM:0000850/ FP 2 /^is_a: EDAM:0001235/ FP 2 /^relationship: / FP 1 /^!/ FC = 128 // ID palindrome-ex AP palindrome IN tembl:d00596 IN 15 IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI d00596.pal FZ = 1579 FP /^Palindromes:\n126 +caaaaaaaaaaaaaaaa +142\n/ FP /^217 +gtttttttttttttttt +201\n/ FP /^127 +aaaaaaaaaaaaaaaagaccgccagggct +155\n/ FP /^204 +ttttttttttttttttctggcggtcccga +176\n/ // # change the examples to use these files ID pasteseq-ex UC To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta': AP pasteseq CL tsw:amir_pseae tsw:flav_nossm -pos=67 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir_pseae.fasta FZ = 275 FP /^FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL\n/ // ID pasteseq-ex2 UC This does the same thing, but the output qualifier is explicitly used: AP pasteseq CL tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amirplus.seq FZ = 275 FP /^FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL\n/ // ID pasteseq-ex3 UC To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0: AP pasteseq CL tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amirplus.seq FZ = 275 FP /^DALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVAL\n/ // ID patmatdb-ex AP patmatdb IN tsw:* IN st[ty]s IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 12s1_arath.patmatdb FC = 80 FP /^# Sequence: HD_TAKRU from: 1 to: 3148\n# HitCount: 1\n/ FP /^Length = 4\n/ FP /^Start = position 1038 of sequence\n/ FP /^End = position 1041 of sequence\n/ FP /^STPASSTTSSAVDP\n/ FP /^# Reported_sequences: 3\n/ FP /^# Reported_hitcount: 3\n/ // ID pepcoil-ex AP pepcoil IN tsw:gcn4_yeast IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI gcn4_yeast.pepcoil FZ = 845 FP 1 /^ +Sequence:/ FP /^\(1\) Score 1\.910 length 49 at residues 233->281\n/ FP /^ Sequence: ARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVGER\n/ OC The SwissProt annotation marks the true leucine zipper motif as from 253 to 274. OC The leucine zipper is a special case of a coiled-coil region. // ID pepdigest-ex AP pepdigest IN tsw:opsd_human IN IN IN FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.pepdigest FP /^ 246 248 346\.384 K E AEK\n/ FP /yields 14 fragments/ FC = 36 // ID pepdigest-range AP pepdigest CL -sbegin 10 -send 250 IN tsw:opsd_human IN IN IN FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.pepdigest FP /^ 246 248 346\.384 K E AEK\n/ FP /yields 8 fragments/ FC = 32 // ID pepinfo-ex AP pepinfo IN tsw:opsd_human IN cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created pepinfo\.ps\n/ FI opsd_human.pepinfo FC = 4248 FP 3 /^\s+4\s+T\s+1\n/ FP 6 /^\s+4\s+T\s+0\n/ FP 3 /^\s+4\s+T\s+0\.000\n/ FI pepinfo.ps FC = 23209 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 2\n/ // ID pepinfo-plot1 AP pepinfo CL -nohydropathyplot IN tsw:opsd_human IN cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created pepinfo\.ps\n/ FI opsd_human.pepinfo FC = 3186 FP 3 /^\s+4\s+T\s+1\n/ FP 6 /^\s+4\s+T\s+0\n/ FP 0 /^\s+4\s+T\s+0\.000\n/ FI pepinfo.ps FC = 22594 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepinfo-plot2 AP pepinfo CL -nogeneralplot IN tsw:opsd_human IN cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created pepinfo\.ps\n/ FI opsd_human.pepinfo FC = 1062 FP 0 /^\s+4\s+T\s+1\n/ FP 0 /^\s+4\s+T\s+0\n/ FP 3 /^\s+4\s+T\s+0\.000\n/ FI pepinfo.ps FC = 709 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepnet-ex AP pepnet CL -sask IN tsw:gcn4_yeast IN 253 IN 274 IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 18 FP /^Created pepnet\.ps\n/ FI pepnet.ps FC = 447 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepnet-data AP pepnet CL -sask -graph data ## No -outfile qualifier - fixed filename IN tsw:gcn4_yeast IN 253 IN 274 FI stdout FC = 1 FP /^Created pepnet1\.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pepnet1.dat FC = 105 FP /^##Maintitle Helical net of tsw-id:GCN4_YEAST\[253:274\]\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^Text1 x1 139\.599991 y1 93\.500000 colour 1 size 0\.750000 D\n/ FP /^Rectangle x1 134\.499985 y1 85\.430000 x2 137\.499985 y2 88\.430000 colour 9\n/ // ID pepstats-keep AP pepstats DL keep IN tsw:laci_ecoli IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.pepstats FZ = 1568 FP /^Molecular weight = 38590\.16/ FP /^Average Residue Weight = 107\.195\s+Charge\s+= 1\.5\s+\n/ FP /^Isoelectric Point = 6\.8820\n/ FP /^A280 Molar Extinction .* = 22920 .* 23045 / FP /^A280 Extinction .* = 0\.594 .* 0\.597 / FP /^Improbability of expression in inclusion bodies = 0\.660\n/ FP /^A = Ala\s+44\s+12\.222\s+1\.421\s+\n/ FP /^Tiny\s+\(A\+C\+G\+S\+T\)\s+120\s+33\.333\n/ // ID makeprotseq-ex2 AP makeprotseq IN ../pepstats-keep/laci_ecoli.pepstats IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI makeseq.fasta FC = 300 FP 100 /^>EMBOSS_[0-9][0-9][0-9]/ FP /\A>EMBOSS_001\neqngievef.*avpdkallvv\nnllvla.*kssnv\n>/ // ID pepwheel-ex AP pepwheel CL tsw:hbb_human -send 30 IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 20 FP /^Created pepwheel\.ps\n/ FI pepwheel.ps FC = 575 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwheel-data AP pepwheel CL tsw:hbb_human -send 30 -graph data FI stdout FC = 1 FP /^Created pepwheel1\.dat\n/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pepwheel1.dat FC = 132 FP /^##Maintitle Helical wheel of tsw-id:HBB_HUMAN\[:30\]\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^Text1 x1 0\.446413 y1 -0\.078715 colour 9 size 1\.000000 V\n/ FP /^Rectangle x1 -0\.025000 y1 0\.431300 x2 0\.025000 y2 0\.481300 colour 9\n/ // ID pepwindow-ex AP pepwindow CL tsw:opsd_human IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created pepwindow\.ps\n/ FI pepwindow.ps FC = 305 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwindow-local AP pepwindow PP EMBOSS_DATA=../aaindexextract-keep/ PP export EMBOSS_DATA CL tsw:opsd_human IN ps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created pepwindow\.ps\n/ FI pepwindow.ps FC = 305 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwindow-localdata AP pepwindow PP EMBOSS_DATA=../aaindexextract-keep/ PP export EMBOSS_DATA CL tsw:opsd_human -datafile chop780101 IN ps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 21 FP /^Created pepwindow\.ps\n/ FI pepwindow.ps FC = 317 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID pepwindow-localfail AP pepwindow ER 1 PP EMBOSS_DATA=../aaindexextract-keep/ PP export EMBOSS_DATA CL tsw:opsd_human -datafile fail780101 IN ps FI stderr FC = 3 FP /^Error: Unable to open data file 'fail780101' for input\n/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // # change example to globins.msf (plural) ID pepwindowall-ex AP pepwindowall CL ../../data/globins.msf -gxtitle="Base Number" -gytitle="hydropathy" IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 24 FP /^Created pepwindowall\.ps\n/ FI pepwindowall.ps FC = 456 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // # change example to use globins.msf ID plotcon-ex AP plotcon CL -sformat msf ../../data/globins.msf -graph cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created plotcon\.ps\n/ FI plotcon.ps FC = 257 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID plotcon-data AP plotcon CL -sformat msf ../../data/globins.msf -graph data IN FI stdout FC = 1 FP /^Created plotcon1\.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI plotcon1.dat FC = 179 FP /^##Points 164\n/ FP /^135\.000000\s+0\.305580\n/ // ID plotorf-ex AP plotorf IN tembl:x13776 IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created plotorf\.ps\n/ FI plotorf.ps FC = 741 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID plotorf-ex2 UC An example of specifying your own START and STOP codons with a mitochondrial sequence would be: AP plotorf CL -start ATT,ATC,ATA,ATG,GTG -stop TAA,TAG,AGA,AGG IN ../../data/mito.seq IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created plotorf\.ps\n/ FI plotorf.ps FC = 6352 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID polydot-ex AP polydot CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta" CL -graph cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created polydot\.ps\n/ FI polydot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID polydot-data AP polydot CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta" CL -graph data IN FI stdout FC = 1 FP /^Created polydot1\.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI polydot1.dat FC = 202 FP /^##Maintitle Polydot of globins.fasta\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^##Screen x1 -163\.350006 y1 -163\.350006 x2 1690\.672485 y2 1252\.349976\n/ FP /^Textline x1 -98\.010010 y1 73\.000000 x2 -98\.010010 y2 146\.000000 colour 0 size 0\.300000 HBB_HUMAN\n/ FP /^Rectangle x1 0\.000000 y1 156\.000000 x2 146\.000000 y2 302\.000000 colour 0\n/ FP /^Text1 x1 1121\.670044 y1 1056\.329956 colour 0 size 0\.300000 No\. Length Lines Points Sequence\n/ FP /^Text1 x1 1121\.670044 y1 1023\.659973 colour 0 size 0\.300000 1 146 8 248 HBB_HUMAN\n/ // ID polydot-feat AP polydot CL ../../data/globins.fasta -gtitle="Polydot of globins.fasta" CL -graph cps -dumpfeat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 19 FP /^Created polydot\.ps\n/ FI polydot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ FI globins.gff FC = 63 FP 7 /^##sequence-region / FP /HBB_HUMAN\s+wordmatch\s+polypeptide_region\s+88\s+111\s+1\.000\s+[+]\s+\.\s+ID=HBB_HUMAN\.1;note=HBB_HORSE\n/ // ID preg-ex AP preg IN tsw:*_rat IN IA[QWF]A IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI arf3_rat.preg FC = 44 FP /^ 421 424 regex: IA\[QWF\]A IAQA\n/ FP /^# Reported_sequences: 2\n/ FP /^# Reported_hitcount: 1\n/ // ID prettyplot-ex AP prettyplot CL -resbreak=10 -boxcol -consensus -plurality=3 IN ../../data/globins.msf IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 22 FP /^Created prettyplot\.ps\n/ FI prettyplot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID prettyplot-ex2 AP prettyplot CL ../../data/globins.msf -plurality=3 -docolour IN cps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 22 FP /^Created prettyplot\.ps\n/ FI prettyplot.ps FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID prettyplot-data AP prettyplot CL -resbreak=10 -boxcol -consensus -plurality=3 CL -graph data IN ../../data/globins.msf FI stdout FC = 4 FP /^Created prettyplot2\.dat\n/ FP 4 /^Created prettyplot\d\.dat\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI prettyplot1.dat FC = 603 FP /^##Maintitle Pretty plot of ..\/..\/data\/globins.msf\n/ FP /^##Subtitle Fri 15 Jul 2011 12:00:00\n/ FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/ FP /^Text1 x1 -10\.000000 y1 36\.619671 colour 0 size 10\.491803 Consensus\n/ FP /^Text1 x1 59\.000000 y1 36\.619671 colour 0 size 10\.491803 50\n/ FP /^Text2 x1 18\.500000 y1 36\.619671 colour 0 size 10\.491803 S\n/ FI prettyplot2.dat FC = 862 FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/ FP /^Text2 x1 1\.500000 y1 36\.619671 colour 0 size 10\.491803 F\n/ FI prettyplot3.dat FC = 815 FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/ FP /^Text2 x1 2\.500000 y1 36\.619671 colour 0 size 10\.491803 H\n/ FI prettyplot4.dat FC = 181 FP /^Text1 x1 -10\.000000 y1 44\.714752 colour 0 size 10\.491803 LGB2_LUPLU\n/ FP /^Text2 x1 3\.500000 y1 36\.619671 colour 0 size 10\.491803 L\n/ // ID prettyseq-ex AP prettyseq IN tembl:x13776 IN 135-1292 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.prettyseq FZ = 8166 FP / 121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180\n/ FP / 1 M G S H Q E R P L I G L L F S E 16\n/ // ID primersearch-ex AP primersearch CL tembl:z52466 IN ../../data/primers IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI z52466.primersearch FZ = 402 FP /^Primer name D1S2660\nAmplimer 1\n/ FP /^\tSequence: Z52466 Z52466 \n/ FP /^\tH\.sapiens \(D1S2660\) DNA segment containing \(CA\) repeat; clone AFMa203yc1; single read\.\n/ FP /^\tCACACATGCACATGCAC hits forward strand at 27 with 0 mismatches\n/ FP /^\tAGTGACACCAGCAGGG hits reverse strand at \[103\] with 0 mismatches\n/ FP /^\tAmplimer length: 261 bp\n/ // ID primersearch-ex2 UC Here we run the same example but allowing 20% mismatch between the primers and the sequence: AP primersearch CL tembl:z52466 IN ../../data/primers IN 20 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI z52466.primersearch FZ = 680 FP /^Amplimer 1\n\tSequence: Z52466 Z52466 \n/ FP /^Amplimer 2\n\tSequence: Z52466 Z52466 \n/ FP /^\tCACACATGCACATGCAC hits forward strand at 49 with 2 mismatches\n/ // ## commit a data/seqs.list file for input ##ID primersearch-ex3 ##UC Here is an example of running with a file containing a list of sequences: ##CC Need the seqs.list input list ##AP primersearch ##CL @../../data/seqs.list ##IN ../../data/primers ##IN ##IN ##FI stderr ##FC = 2 ##FP 0 /Warning: / ##FP 0 /Error: / ##FP 0 /Died: / ##FI hs214yg7.primersearch ##FZ = 0 ##// ID printsextract-keep DL keep PP mkdir ./PRINTS PP EMBOSS_DATA=./ PP export EMBOSS_DATA AP printsextract IN ../../data/prints.test FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI PRINTS // ID profit-ex AP profit ## changed to a matrix file which produces some results ##IN ../../data/globins.prophecy IN ../../data/outfile.prophecy IN tsw:* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.profit FZ = 180 FP /^HBB_HUMAN/ // ID prophecy-ex AP prophecy IN ../../data/globins.msf IN IN globins IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.prophecy FZ = 13782 FC = 173 FP /^Maximum score\s+496\n/ FP /^Consensus\s+PIVDT.*AAYQG\n/ // ID prophecy-ex2 AP prophecy IN ../../data/globins.msf IN g IN IN globins IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.prophecy ## ## Do not check file size. AIX reports -0.00 in some positions ## so the file can be slightly larger ## FP /^Max_score\s+939\.76\n/ FP /^Consensus\s+PIVDT.*ELGYQG\n/ FP /^0\.65 0\.00 0\.13 0\.13 0\.13 -0\.78 .* 0\.87 0\.87\n/ // # example - use h* to save time ID prophet-ex TI 600 AP prophet IN tsw:h* IN ../../data/globins.gribskov IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.prophet FP /^# Score: 161\.14\n/ FP /^globins +15 ELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLS +64\n/ FP /^HBA_HUMAN +2 VLSPADKTNVKAAW-GKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS +50\n/ // ID prosextract-keep AP prosextract DL keep PP mkdir ./PROSITE PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI PROSITE // ID patmatmotifs-ex AP patmatmotifs PP EMBOSS_DATA=../prosextract-keep/ PP export EMBOSS_DATA CL -full IN tsw:opsd_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.patmatmotifs FP /^# HitCount: 2\n/ FP /^# Motif: OPSIN\n# Count: 1\n/ FP /^Start = position 123 of sequence\n/ FP /^End = position 139 of sequence\n/ FP /^Length = 17\n/ FP /^Motif = G_PROTEIN_RECEP_F1_1\n/ FP /^TLGGEIALWSLVVLAIERYVVVCKPMS\n/ // ID pscan-ex AP pscan PP EMBOSS_DATA=../printsextract-keep/ PP export EMBOSS_DATA IN tsw:opsd_human IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI opsd_human.pscan FZ = 871 FP /^Fingerprint GPCRRHODOPSN Elements 7\n Accession number PR00237\n/ FP /^ Element 2 Threshold 49% Score 75%\n/ FP /^ Start position 72 Length 22\n/ FP /^ Element 1 Threshold 54% Score 64%\n/ FP /^ Start position 39 Length 25\n/ // ID psiphi-ex AP psiphi CL ../../data/1hmp_a.ccf -chainnumber=1 -startresiduenumber=5 -finishresiduenumber=85 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 1hmp_a.psiphi FZ = 3843 FP / 56 56 0\.0 \-139\.15 162\.01\n/ // ID rebaseextract-keep AP rebaseextract DL keep PP mkdir ./REBASE PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/withrefm IN ../../data/proto FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / DI REBASE DF embossre.enz DF embossre.equ DF embossre.ref DF embossre.sup // ID recoder-ex AP recoder PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:x65923 IN EcoRII IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.recoder FC = 72 FP 3 / +77 +81 +[+] . +EcoRII +CCWGG +78 +P\.P +C->[ACGT]\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 34\n/ // ID recoder-seqs AP recoder PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -sshow -tshow IN tembl:x65923 IN EcoRII IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.recoder FC = 108 FP 3 / +77 +81 +[+] . +EcoRII +CCWGG +78 +P\.P +C->[ACGT]\n/ FP /# 61 +AGCTCTTTGT CCGCGCCCAG GAGCTACACA CCTTCGAGGT GACCGGCCAG GAAACGGTCG \n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 34\n/ // # make bamhi explicit in reply to prompt ID redata-ex AP redata PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN BamHI IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.redata FP /\ABamHI\n/ FP /^Recognition site is GGATCC leaving sticky ends\n/ FP /^ Cut positions 5':1 3':5\n/ // ID remap-ex UC This example uses only a small region of the input sequence to save space. UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 IN tembl:j01636 IN taqi,bsu6i,acii,bsski IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.remap FZ = 1228 FP /^# Enzymes that cut.*\n(\s+\S+\s+1\s+\S*\n){4}\n/ FP /^# Enzymes that do not cut.*\n\n/ FP /^\s+AciI\s+1\s+\n/ FP /^\s+BssKI\s+1\s+\n/ FP /^\s+Ksp632I\s+1\s+Bsu6I\n/ FP /^\s+TaqI\s+1\s+\n/ // ID remap-ex2 UC This is an example where all enzymes in the REBASE database are used, UC (but only the prototypes of the isoschizomers are reported by default). UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 IN tembl:j01636 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.remap FZ = 1850 FP /^\s+Hin6I\s+2\s+HinP1I,HspAI\n/ // ID remap-ex3 UC This is an example where all enzymes in the REBASE database are used UC but the -limit qualifier is not set so that all of the enzymes are UC displayed and not just only the prototypes of the isoschizomers. UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 -nolimit IN tembl:j01636 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.remap FZ = 2412 FP /^\s+TaqI\s+1\s+\n/ // ID remap-ex4 UC This shows the 'flat' format: UC This is run with a small test version of the restriction enzyme database UC and so you will probably see more enzymes when you run this. AP remap PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -notran -sbeg 1 -send 60 -flat IN tembl:j01636 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.remap FZ = 2244 FP /^\s+Hin6I\s+2\s+HinP1I,HspAI\n/ // ID restover-ex AP restover PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:x65923 IN cg IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.restover FZ = 1123 FP /^# Number of hits with any overlap: 54\n/ FP /^\s+11\s+TaqI\s+TCGA\s+11\s+13\s+\n/ // ID restrict-ex AP restrict PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:x65923 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.restrict FP /^\s+11\s+14\s+[+]\s+TaqI\s+TCGA\s+11\s+13\s+\.\s+\.\n/ FP /^\s+125\s+135\s+[+]\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+148\s+143\n/ // ID restrict-ex2 UC This gives the lengths of the restriction fragments produced by UC cutting with all of the specified enzymes. AP restrict CL -fragments PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:x65923 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.restrict FP /^\s+11\s+14\s+[+]\s+TaqI\s+TCGA\s+11\s+13\s+\.\s+\.\n/ FP /^\s+125\s+135\s+[+]\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+148\s+143\n/ FP /^#\s+79/ // ID restrict-ex3 UC This gives the lengths of the restriction fragments created by UC cutting with just one of each of the specified enzymes in turn. AP restrict CL -solofragment PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA IN tembl:x65923 IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.restrict FP /^\s+11\s+14\s+[+]\s+TaqI\s+TCGA\s+11\s+13\s+\.\s+\.\n/ FP /^\s+125\s+135\s+[+]\s+Hin4I\s+GAYNNNNNVTC\s+116\s+111\s+148\s+143\n/ FP /^#\s+3\s+13\s+25\s+33\s+37\s+114/ // ID restrict-nonpal UC Tests non-palindromic sites AP restrict PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA CL -enzymes BseYI IN asis:GCTGGGTTTCCCAGC IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI asis.restrict FP /^\s+1\s+6\s+[-]\s+BseYI\s+CCCAGC\s+1\s+5\s+\.\s+\.\n/ FP /^\s+10\s+15\s+[+]\s+BseYI\s+\CCCAGC\s+10\s+14\s+\.\s+\.\n/ // ID revseq-ex UC To create the reverse complement (reverse sense) of 'tembl:x65923' in the file 'x65923.rev': AP revseq CL tembl:x65923 x65923.rev FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.rev FZ = 573 FP /^>X65923 X65923\.1 Reversed: H\.sapiens fau mRNA\n/ FP /^gtcccagctaccgcgaagatggagtcgagaaagaggaa\n/ // ID revseq-ex2 UC To create the complement of 'tembl:x65923' in the file 'x65923.rev': AP revseq CL tembl:x65923 x65923.rev -norev FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.rev FZ = 563 FP /^agattattttttcggtgaatcaagtcagtttttttttt\n/ // ID revseq-ex3 UC To create the reverse of 'tembl:x65923' in the file 'x65923.rev': AP revseq CL tembl:x65923 x65923.rev -nocomp FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.rev FZ = 563 FP /^cagggtcgatggcgcttctacctcagctctttctcctt\n/ // ID seealso-ex AP seealso IN matcher FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP /^seqmatchall/ FP /^supermatcher/ FP /^water/ FP /^wordfinder/ FP /^wordmatch/ // ID seqcount-ex AP seqcount CL "tembl:*" -out tembl.seqcount FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI tembl.seqcount FC = 1 FP /^49\n/ // ID seqmatchall-ex UC Here is an example using an increased word size to avoid accidental matches: AP seqmatchall IN @../../data/eclac.list IN 15 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.seqmatchall FZ = 1623 FP /^ 1832 J01636 +[+] +5646\.\.7477 X51872 +[+] +1\.\.1832\n/ FP /^ 1113 J01636 +[+] +49\.\.1161 V00294 +[+] +1\.\.1113\n/ FP /^ 1500 J01636 +[+] +4305\.\.5804 V00295 +[+] +1\.\.1500\n/ FP /^ 3078 J01636 +[+] +1287\.\.4364 V00296 +[+] +1\.\.3078\n/ FP /^ 159 X51872 +[+] +1\.\.159 V00295 +[+] +1342\.\.1500\n/ FP /^ 60 V00295 +[+] +1\.\.60 V00296 +[+] +3019\.\.3078\n/ // ########################################################################### # first entry in first file ID seqret-dbidfilefirst AP seqret CL -auto tembl:H45989 test.out FI test.out FP 1 /\A>H45989 / // # last entry in last file ID seqret-dbidfilelast AP seqret CL -auto tembl-id:U23808 test.out FI test.out FP 1 /\A>U23808 / // # last entry in last file ID seqret-dbacfilelast AP seqret CL -auto tembl-acc:U23808 test.out FI test.out FP 1 /\A>U23808 U23808\.2 / // ID seqret-dbacfirst AP seqret CL -auto tembl-acc:AB000095 test.out FI test.out FP 1 /\A>AB000095 AB000095\.1 / // ID seqret-dbacnextlast AP seqret CL -auto tembl-acc:Z52466 test.out FI test.out FP 1 /\A>Z52466 Z52466\.1 / // ID seqret-dbaclast AP seqret CL -auto tembl-acc:Z69719 test.out FI test.out FP 1 /\A>Z69719 Z69719\.1 / // ########################################################################## # # sequence input formats ... specified with -sformat and as -inauto # also preferably as -inmulti # where FASTA can check handling of various IDs # could test with infoseq for length/id/acc/org # # todo: # swiss (sw swissprot) # pdb # pdbseq # pbdnuc # pdbnucseq # gifasta # pearson # fastq # fastq-sanger # fastq-solexa # fastq-illumina # sam # refseq # refseqp # genpept # ace # consed # dbid # hennig86 # jackknifer # nexus (paup) # treecon # mega # igstrict # ig (no auto detect) # asis # gff2 # gff3 # biomart # bam # ensembl # das # # also various fasta ids (test what ID is returned) # # # also output formats (similar list) # # also seq+feature for thse which support features # also nuc+prot if appropriate # # also sets of sets (phylip etc.) is multiset. # # script to process entrails output, check test names. # ########################################################################## ID seq-inlist-good AP seqret CL -auto @../../data/good.list test.out -osf swiss FI test.out FZ = 599 FP 3 /^ID .* AA\.\n/ FP /^SQ SEQUENCE 56 AA; 6465 MW; 48CB2E252357CBF6 CRC64;/ // ID seq-inlist-bad AP seqret CL -auto @../../data/bad.list test.out -osf swiss FI stderr FZ = 112 FP 0 /Warning: / FP 2 /Error: / FP 0 /Died: / FP /^Error: Failed to open filename '\.\.\/\.\.\/data\/alignc\.prot'\n/ FP /^Error: Failed to read sequence '\.\.\/\.\.\/data\/alignc\.prot'\n/ FI test.out FP 3 /^ID .* AA\.\n/ FP /^SQ SEQUENCE 56 AA; 6465 MW; 48CB2E252357CBF6 CRC64;/ // ID seq-inlist-ugly AP seqret CL -auto @../../data/ugly.list test.out -osf embl FI stderr FZ = 47 FP /^Error: Failed to read sequence 'tembl:V002944'\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seq-inlist-uglyfirst AP seqret CL -auto @../../data/uglyfirst.list test.out -osf embl FI stderr FZ = 47 FP /^Error: Failed to read sequence 'tembl:V002944'\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seq-inlist-uglylast AP seqret CL -auto @../../data/uglylast.list test.out -osf embl FI stderr FZ = 47 FP /^Error: Failed to read sequence 'tembl:V002944'\n/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seq-inlist-uglyall AP seqret CL -auto @../../data/uglyall.list test.out -osf embl FI stderr FZ = 141 FP /^Error: Failed to read sequence 'tembl:V002943'\n/ FP /^Error: Failed to read sequence 'tembl:V002944'\n/ FP /^Error: Failed to read sequence 'tembl:V002945'\n/ FP 0 /Warning: / FP 3 /Error: / FP 0 /Died: / FI test.out FP 2 /^ID .* BP\.\n/ FP /^SQ Sequence 3078 BP; 682 A; 841 C; 886 G; 669 T; 0 other;/ // ID seq-inlist-testdb AP seqret CL -auto @../../data/testdb.list test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/ FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/ FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/ FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/ // ID seq-inlist-testdb-sbegin AP seqret CL -auto @../../data/testdb.list -sbegin 11 test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/ FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/ FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/ FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/ // ID seq-inlist-testdb-send AP seqret CL -auto @../../data/testdb.list -send -11 test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/ FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/ FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/ FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/ // ID seq-inlist-testdb-strim AP seqret CL -auto @../../data/testdb.list -sbegin 11 -send -11 test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/ FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/ FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/ FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/ // ID seq-inlist-testdb-strimrev AP seqret CL -auto @../../data/testdb.list -sbegin 11 -send -11 -srev test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nTTTTGGGGCCCAAATTGGCAGTAACCGGGTTTAAAACCCC\n/ FP />TCGAseq [^\n]+\nAAAAGGGGCCCTTTAAGGCTGATTCCGGGAAATTTTCCCC\n/ FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/ FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/ // ID seq-set-inlist-testdb AQ seqretset CL -auto @../../data/testdb.list test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/ FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/ FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/ FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/ // ID seq-set-inlist-testdb-sbegin AQ seqretset CL -auto @../../data/testdb.list -sbegin 11 test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAATTTTTGGGGG\n/ FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTTAAAAAGGGGG\n/ FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTTCCCCCAAAAA\n/ FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAACCCCCTTTTT\n/ // ID seq-set-inlist-testdb-send AQ seqretset CL -auto @../../data/testdb.list -send -11 test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nAAAAACCCCCGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/ FP />TCGAseq [^\n]+\nTTTTTCCCCCGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/ FP />TGACseq [^\n]+\nTTTTTGGGGGAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/ FP />AGTCseq [^\n]+\nAAAAAGGGGGTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/ // ID seq-set-inlist-testdb-strim AQ seqretset CL -auto @../../data/testdb.list -sbegin 11 -send -11 test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nGGGGTTTTAAACCCGGTTACTGCCAATTTGGGCCCCAAAA\n/ FP />TCGAseq [^\n]+\nGGGGAAAATTTCCCGGAATCAGCCTTAAAGGGCCCCTTTT\n/ FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/ FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/ // ID seq-set-inlist-testdb-strimrev AQ seqretset CL -auto @../../data/testdb.list -sbegin 11 -send -11 -srev test.out -osf fasta FI test.out FP 4 /^>/ FP />ACGTseq [^\n]+\nTTTTGGGGCCCAAATTGGCAGTAACCGGGTTTAAAACCCC\n/ FP />TCGAseq [^\n]+\nAAAAGGGGCCCTTTAAGGCTGATTCCGGGAAATTTTCCCC\n/ FP />TGACseq [^\n]+\nAAAACCCCTTTGGGAACCTGCAGGTTCCCAAAGGGGTTTT\n/ FP />AGTCseq [^\n]+\nTTTTCCCCAAAGGGTTCCAGCTGGAACCCTTTGGGGAAAA\n/ // ID seq-inauto-acedb AP seqret CL -auto ../../data/dna.acedb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-acedb AP seqret CL -auto acedb::../../data/dna.acedb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-acedb AP seqret CL -auto ../../data/dna.acedb -sf acedb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-codata AP seqret CL -auto ../../data/dna.codata test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-codata AP seqret CL -auto codata::../../data/dna.codata test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-codata AP seqret CL -auto ../../data/dna.codata -sf codata test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-embl AP seqret CL -auto ../../data/dna.embl test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-embl AP seqret CL -auto embl::../../data/dna.embl test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-embl AP seqret CL -auto ../../data/dna.embl -sf embl test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-em AP seqret CL -auto ../../data/dna.embl -sf em test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-experiment AP seqret CL -auto ../../data/xb63c7.s1.exp test.out -osf embl FI test.out FP /^ID .* 439 BP\.\n/ FP /^SQ Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/ // ID seq-inusa-experiment AP seqret CL -auto experiment::../../data/xb63c7.s1.exp test.out -osf embl FI test.out FP /^ID .* 439 BP\.\n/ FP /^SQ Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/ // ID seq-in-experiment AP seqret CL -auto ../../data/xb63c7.s1.exp -sf experiment test.out -osf embl FI test.out FP /^ID .* 439 BP\.\n/ FP /^SQ Sequence 439 BP; 162 A; 53 C; 61 G; 153 T; 10 other;/ // ID seq-inauto-fasta AP seqret CL -auto ../../data/dna.fasta test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-fasta AP seqret CL -auto fasta::../../data/dna.fasta test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-fasta AP seqret CL -auto ../../data/dna.fasta -sf fasta test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-innuc-fasta AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/dna.fasta -snuc -sf fasta -outfile test.out FI test.out FC = 2 FP /^fasta::\S+\t-\tFASTA\tF10002\tN\t100\t/ // ID seq-inprot-fasta AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/prot.fasta -sprot -sf fasta -outfile test.out FI test.out FC = 2 FP /^fasta::\S+\t-\tFASTA\tF00001\tP\t100\t/ // ID seq-in-fastq AP seqret CL -auto ../../data/fastqall.sanger -sf fastq test.out -osf experiment FI test.out FC = 5 FP /^ID .* 94 BP\.\n/ FP /^SQ Sequence 94 BP; 24 A; 24 C; 23 G; 23 T; 0 other;/ // ID seq-inauto-fastq AP seqret CL -auto ../../data/fastqall.sanger test.out -osf experiment FI test.out FC = 5 FP /^ID .* 94 BP\.\n/ FP /^SQ Sequence 94 BP; 24 A; 24 C; 23 G; 23 T; 0 other;/ // ID seq-in-fastq-illumina AP seqret CL -auto ../../data/fastqall.illumina13 -sf fastq-illumina test.out -osf experiment FI test.out FC = 7 FP /^ID .* 41 BP\.\n/ FP /^AV 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1\n/ FP /^SQ Sequence 41 BP; 11 A; 10 C; 10 G; 10 T; 0 other;\n/ // ID seq-in-fastq-sanger AP seqret CL -auto ../../data/fastqall.sanger -sf fastq-sanger test.out -osf experiment FI test.out FC = 10 FP /^ID .* 94 BP\.\n/ FP /^AV 73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 55 54\n/ FP /^SQ Sequence 94 BP; 24 A; 24 C; 23 G; 23 T; 0 other;\n/ // ID seq-in-fastq-solexa AP seqret CL -auto ../../data/fastqall.solexa -sf fastq-solexa test.out -osf experiment FI test.out FC = 7 FP /^ID .* 46 BP\.\n/ FP /^AV 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 6 5 4 4 3\n/ FP /^SQ Sequence 46 BP; 12 A; 12 C; 11 G; 11 T; 0 other;\n/ // ID seq-inauto-gcg AP seqret CL -auto ../../data/dna.gcg test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-gcg AP seqret CL -auto gcg::../../data/dna.gcg test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-gcg AP seqret CL -auto ../../data/dna.gcg -sf gcg test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-innuc-gcg AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/dna.gcg -snuc -sf gcg -outfile test.out FI test.out FC = 2 FP /^gcg::\S+\t-\tGCG\t-\tN\t100\t/ // ID seq-inprot-gcg AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/prot.gcg -sf gcg -outfile test.out FI test.out FC = 2 FP /^gcg::\S+\t-\tGCG\t-\tP\t100\t/ // ID seq-inauto-gcg8 AP seqret CL -auto ../../data/dna.gcg8 test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-gcg8 AP seqret CL -auto gcg8::../../data/dna.gcg8 test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-gcg8 AP seqret CL -auto ../../data/dna.gcg8 -sf gcg8 test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-genbank AP seqret CL -auto ../../data/dna.genbank test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-genbank AP seqret CL -auto genbank::../../data/dna.genbank test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-genbank AP seqret CL -auto ../../data/dna.genbank -sf genbank test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-gb AP seqret CL -auto ../../data/dna.genbank -sf gb test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-ddbj AP seqret CL -auto ../../data/dna.genbank -sf ddbj test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-genpept AP seqret CL -auto ../../data/acn78416.genpept -sf genpept test.out -osf swiss CC reference number and range only, no details parsed FI test.out FC = 15 FP /^ID .* 165 AA\.\n/ FP /^DT 21-MAR-2009, entry version 1.\n/ FP /^SQ SEQUENCE 165 AA; 18854 MW; 75F27E4168A4FAE7 CRC64;\n/ // ID seq-in-gifasta AP seqret CL -auto ../../data/ncbi.gifasta -sf gifasta test.out -osf swiss FI test.out FP /^ID .* 8 AA\.\n/ FP /^SQ SEQUENCE 8 AA; 950 MW; 61E059CB04176058 CRC64;/ // ID seq-innuc-gifasta AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/ncbinuc.gifasta -snuc -sf gifasta -outfile test.out FI test.out FC = 2 FP /^gifasta::\S+\t-\t123456\t-\tN\t8\t/ // ID seq-inprot-gifasta AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/ncbi.gifasta -sprot -sf gifasta -outfile test.out FI test.out FC = 2 FP /^gifasta::\S+\t-\t123456\t-\tP\t8\t/ // ID seq-inauto-ig AP seqret CL -auto ../../data/dna.ig test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-ig AP seqret CL -auto ig::../../data/dna.ig test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-ig AP seqret CL -auto ../../data/dna.ig -sf ig test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-ncbi AP seqret CL -auto ../../data/dna.ncbi test.out -osf embl FI test.out FP /^ID .* 100 BP/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-ncbi AP seqret CL -auto ncbi::../../data/dna.ncbi test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-ncbi AP seqret CL -auto ../../data/dna.ncbi -sf ncbi test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-nbrf AP seqret CL -auto ../../data/prot.nbrf test.out -osf swiss FI test.out FZ = 251 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9685 MW; 5B548D9C397EC1FE CRC64;/ // ID seq-inusa-nbrf AP seqret CL -auto nbrf::../../data/prot.nbrf test.out -osf swiss FI test.out FZ = 251 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9685 MW; 5B548D9C397EC1FE CRC64;/ // ID seq-in-nbrf AP seqret CL -auto ../../data/prot.nbrf -sf nbrf test.out -osf swiss FI test.out FZ = 251 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9685 MW; 5B548D9C397EC1FE CRC64;/ // ID seq-innuc-nbrf AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/dna.nbrf -snuc -sf nbrf -outfile test.out FI test.out FC = 2 FP /^nbrf::\S+\t-\tGENBANK\t-\tN\t100\t/ // ID seq-inprot-nbrf AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/prot.nbrf -sprot -sf nbrf -outfile test.out FI test.out FC = 2 FP /^nbrf::\S+\t-\tpir\t-\tP\t90\t/ // ID seq-in-pir AP seqret CL -auto ../../data/prot.nbrf -sf pir test.out -osf swiss FI test.out FZ = 251 FP /^ID pir .* 90 AA\.\n/ FP /^DE example pir format\n/ FP /^SQ SEQUENCE 90 AA; 9685 MW; 5B548D9C397EC1FE CRC64;/ // ID seq-in-pdb AP seqret CL -auto ../../data/1tos.pdb -sf pdb test.out -osf swiss CC PDB format reads all 3 models FI test.out FZ = 396 FP /^ID 1TOS_A1 .* 10 AA\.\n/ FP 3 /^ID 1TOS_A\d .* 10 AA\.\n/ FP /^SQ SEQUENCE 10 AA; 1063 MW; 316593786B5AADC7 CRC64;/ // ID seq-in-pdbnuc AP seqret CL -auto ../../data/133d.pdb -sf pdbnuc test.out -osf embl CC PDBNUC format reads single seqres FI test.out FZ = 390 FP 2 /^ID 133D_[A-Z]; .* 5 BP\.\n/ FP 1 /^ID 133D_A; .* 5 BP\.\n/ FP /^SQ Sequence 5 BP; 0 A; 2 C; 3 G; 0 T; 0 other;/ // ID seq-in-pdbnucseq AP seqret CL -auto ../../data/133d.pdb -sf pdbnucseq test.out -osf embl CC PDBNUC format reads single seqres FI test.out FZ = 390 FP 2 /^ID 133D_[A-Z]; .* 5 BP\.\n/ FP 1 /^ID 133D_A; .* 5 BP\.\n/ FP /^SQ Sequence 5 BP; 0 A; 2 C; 3 G; 0 T; 0 other;/ // ID seq-in-pdbseq AP seqret CL -auto ../../data/1tos.pdb -sf pdbseq test.out -osf swiss CC PDBSEQ format reads single seqres FI test.out FZ = 132 FP /^ID 1TOS_A .* 10 AA\.\n/ FP 1 /^ID 1TOS_A.* 10 AA\.\n/ FP /^SQ SEQUENCE 10 AA; 1063 MW; 316593786B5AADC7 CRC64;/ // ID seq-inauto-pdb AP seqret CL -auto ../../data/1tos.pdb test.out -osf swiss CC PDB format reads single seqres FI test.out FZ = 396 FP /^ID 1TOS_A1 .* 10 AA\.\n/ FP 3 /^ID 1TOS_A\d .* 10 AA\.\n/ FP /^SQ SEQUENCE 10 AA; 1063 MW; 316593786B5AADC7 CRC64;/ // ID seq-in-pearson AP seqret CL -auto ../../data/ncbi.gifasta -sf pearson test.out -osf swiss FI test.out FP /^ID gi[\|]123456.* 8 AA\.\n/ FP /^SQ SEQUENCE 8 AA; 950 MW; 61E059CB04176058 CRC64;/ // ID seq-innuc-pearson AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/ncbinuc.gifasta -snuc -sf pearson -outfile test.out FI test.out FC = 2 FP /^pearson::\S+\t-\tgi\|123456\t-\tN\t8\t/ // ID seq-inprot-pearson AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/ncbi.gifasta -sprot -sf pearson -outfile test.out FI test.out FC = 2 FP /^pearson::\S+\t-\tgi\|123456\t-\tP\t8\t/ // ID seq-inauto-raw AP seqret CL -auto ../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-raw AP seqret CL -auto raw::../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-raw AP seqret CL -auto ../../data/dna.text -sf raw test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-refseq AP seqret CL -auto ../../data/pao-short.refseq -sf refseq test.out -osf embl FI test.out FP /^ID .* 7004 BP\.\n/ FP /^SQ Sequence 7004 BP; 1431 A; 2216 C; 2102 G; 1255 T; 0 other;/ // ID seq-in-refseq-genbank AP seqret CL -auto ../../data/pao-short.refseq -sf genbank test.out -osf embl FI test.out FP /^ID .* 7004 BP\.\n/ FP /^SQ Sequence 7004 BP; 1431 A; 2216 C; 2102 G; 1255 T; 0 other;/ // ID seq-in-refseqp AP seqret CL -auto ../../data/protein.refseqp -sf refseqp test.out -osf swiss CC reference number and range only, no details parsed FI test.out FC = 32 FP /^ID .* 182 AA\.\n/ FP /^SQ SEQUENCE 182 AA; 22127 MW; C7B1D95FB43A4A3F CRC64;\n/ // ID seq-in-sam AP seqret CL -auto ../../data/xxx.sam -sf sam test.out -osf embl FI test.out FP /^ID read_28833_29006_6945;.* 35 BP\.\n/ FP 2 /^ID / FP /^SQ Sequence 35 BP; 6 A; 9 C; 8 G; 12 T; 0 other;\n/ // ID seq-inauto-sam AP seqret CL -auto ../../data/xxx.sam test.out -osf embl FI test.out FP /^ID read_28833_29006_6945;.* 35 BP\.\n/ FP 2 /^ID / FP /^SQ Sequence 35 BP; 6 A; 9 C; 8 G; 12 T; 0 other;\n/ // ID seq-innuc-sam AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/xxx.sam -sf sam -outfile test.out FI test.out FC = 3 FP /^sam::\S+\t-\tread_28833_29006_6945\t-\tN\t35\t48\.57/ FP /^sam::\S+\t-\tread_28701_28881_323b\t-\tN\t35\t57\.14/ // ID seq-inauto-staden AP seqret CL -auto ../../data/dna.staden test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-staden AP seqret CL -auto staden::../../data/dna.staden test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-staden AP seqret CL -auto ../../data/dna.staden -sf staden test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-strider AP seqret CL -auto ../../data/dna.strider test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-strider AP seqret CL -auto strider::../../data/dna.strider test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-strider AP seqret CL -auto ../../data/dna.strider -sf strider test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-swiss AP seqret CL -auto ../../data/amir.swiss -sf swiss test.out -osf swiss FI test.out FP /^ID AMIR_PSEAE .*Reviewed; *196 AA\.\n/ FP /^SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;/ // ID seq-in-sw AP seqret CL -auto ../../data/amir.swiss -sf sw test.out -osf swiss FI test.out FP /^ID AMIR_PSEAE .*Reviewed; *196 AA\.\n/ FP /^SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;/ // ID seq-in-swissprot AP seqret CL -auto ../../data/amir.swiss -sf swissprot test.out -osf swiss FI test.out FP /^ID AMIR_PSEAE .*Reviewed; *196 AA\.\n/ FP /^SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;/ // ID seq-inauto-swiss AP seqret CL -auto ../../data/amir.swiss test.out -osf swiss FI test.out FP /^ID AMIR_PSEAE .*Reviewed; *196 AA\.\n/ FP /^SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;/ // ID seq-inauto-textonly AP seqret CL -auto ../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inusa-textonly AP seqret CL -auto textonly::../../data/dna.text test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-textonly AP seqret CL -auto ../../data/dna.text -sf textonly test.out -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-inauto-abi AP seqret CL -auto ../../data/abiview.abi test.out -osf embl FI test.out FZ = 1265 FP /^ID .* 838 BP\.\n/ FP /^SQ Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/ // ID seq-inusa-abi AP seqret CL -auto abi::../../data/abiview.abi test.out -osf embl FI test.out FZ = 1265 FP /^ID .* 838 BP\.\n/ FP /^SQ Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/ // ID seq-in-abi AP seqret CL -auto ../../data/abiview.abi -sf abi test.out -osf embl FI test.out FZ = 1265 FP /^ID .* 838 BP\.\n/ FP /^SQ Sequence 838 BP; 274 A; 140 C; 182 G; 211 T; 31 other;/ // ID seq-in-unknown AP seqret CL -auto ../../data/dna.text test.out -sf unknown -osf embl FI test.out FP /^ID .* 100 BP\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-innuc-unknown AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/dna.text -snuc -outfile test.out -sf unknown FI test.out FC = 2 FP /^raw::\S+\t-\t-\t-\tN\t100\t/ // ID seq-inprot-unknown AP infoseq CL -nocolumn -delimiter '\t' CL -auto ../../data/prot.text -sprot -outfile test.out -sf unknown FI test.out FC = 2 FP /^raw::\S+\t-\t-\t-\tP\t100\t/ // ID seq-inusa-selex AP seqret CL -auto selex::../../data/test.selex test.out -osf embl FI test.out FZ = 587 FP 3 /^ID/ FP /^ID lig28.* 31 BP\.\n/ FP /^SQ Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/ // ID seq-in-selex AP seqret CL -auto ../../data/test.selex -sf selex test.out -osf embl FI test.out FZ = 587 FP 3 /^ID/ FP /^ID lig28.* 31 BP\.\n/ FP /^SQ Sequence 31 BP; 7 A; 7 C; 8 G; 7 T; 2 other;/ // ID seq-inmultiauto-acedb AP seqret CL -auto ../../data/dna.m-acedb test.out -osf embl FI test.out FP 1 /^ID ACEDBM1; .* 120 BP\.\n/ FP 1 /^ID ACEDBM2; .* 120 BP\.\n/ FP 1 /^ID ACEDBM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-acedb AP seqret CL -auto acedb::../../data/dna.m-acedb test.out -osf embl FI test.out FP 1 /^ID ACEDBM1; .* 120 BP\.\n/ FP 1 /^ID ACEDBM2; .* 120 BP\.\n/ FP 1 /^ID ACEDBM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-acedb AP seqret CL -auto ../../data/dna.m-acedb -sf acedb test.out -osf embl FI test.out FP 1 /^ID ACEDBM1; .* 120 BP\.\n/ FP 1 /^ID ACEDBM2; .* 120 BP\.\n/ FP 1 /^ID ACEDBM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-in-clustal AP seqret CL -auto ../../data/globins.m-aln -sf clustal test.out -osf swiss FI test.out FP 1 /^ID HBB_HUMAN .* 167 AA\.\n/ FP 1 /^ID HBA_HUMAN .* 167 AA\.\n/ FP 7 /^ID / FP 7 /^SQ SEQUENCE \d+ AA; \d+ MW; \S+ CRC64;\n/ FP 1 /^SQ SEQUENCE 167 AA; 15867 MW; BEAE9EB4529C39C3 CRC64;\n/ // ID seq-inauto-clustal AP seqret CL -auto ../../data/globins.m-aln test.out -osf swiss FI test.out FP 1 /^ID HBB_HUMAN .* 167 AA\.\n/ FP 1 /^ID HBA_HUMAN .* 167 AA\.\n/ FP 7 /^ID / FP 7 /^SQ SEQUENCE \d+ AA; \d+ MW; \S+ CRC64;\n/ FP 1 /^SQ SEQUENCE 167 AA; 15867 MW; BEAE9EB4529C39C3 CRC64;\n/ // ID seq-in-aln AP seqret CL -auto ../../data/globins.m-aln -sf aln test.out -osf swiss FI test.out FP 1 /^ID HBB_HUMAN .* 167 AA\.\n/ FP 1 /^ID HBA_HUMAN .* 167 AA\.\n/ FP 7 /^ID / FP 7 /^SQ SEQUENCE \d+ AA; \d+ MW; \S+ CRC64;\n/ FP 1 /^SQ SEQUENCE 167 AA; 15867 MW; BEAE9EB4529C39C3 CRC64;\n/ // ID seq-inmultiauto-aln AP seqret CL -auto ../../data/globins.m-aln test.out -osf swiss FI test.out FP 1 /^ID HBB_HUMAN .* 167 AA\.\n/ FP 1 /^ID HBA_HUMAN .* 167 AA\.\n/ FP 7 /^ID / FP 7 /^SQ SEQUENCE \d+ AA; \d+ MW; \S+ CRC64;\n/ FP 1 /^SQ SEQUENCE 167 AA; 15867 MW; BEAE9EB4529C39C3 CRC64;\n/ // ID seq-inmultiusa-aln AP seqret CL -auto aln::../../data/globins.m-aln test.out -osf swiss FI test.out FP 1 /^ID HBB_HUMAN .* 167 AA\.\n/ FP 1 /^ID HBA_HUMAN .* 167 AA\.\n/ FP 7 /^ID / FP 7 /^SQ SEQUENCE \d+ AA; \d+ MW; \S+ CRC64;\n/ FP 1 /^SQ SEQUENCE 167 AA; 15867 MW; BEAE9EB4529C39C3 CRC64;\n/ // ID seq-inmulti-aln AP seqret CL -auto ../../data/globins.m-aln -sf aln test.out -osf swiss FI test.out FP 1 /^ID HBB_HUMAN .* 167 AA\.\n/ FP 1 /^ID HBA_HUMAN .* 167 AA\.\n/ FP 7 /^ID / FP 7 /^SQ SEQUENCE \d+ AA; \d+ MW; \S+ CRC64;\n/ FP 1 /^SQ SEQUENCE 167 AA; 15867 MW; BEAE9EB4529C39C3 CRC64;\n/ // ID seq-inmultiauto-clustal AP seqret CL -auto ../../data/dna.m-clustal test.out -osf embl FI test.out FP 1 /^ID ALNM1; .* 120 BP\.\n/ FP 1 /^ID ALNM2; .* 120 BP\.\n/ FP 1 /^ID ALNM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-clustal AP seqret CL -auto clustal::../../data/dna.m-clustal test.out -osf embl FI test.out FP 1 /^ID ALNM1; .* 120 BP\.\n/ FP 1 /^ID ALNM2; .* 120 BP\.\n/ FP 1 /^ID ALNM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-clustal AP seqret CL -auto ../../data/dna.m-clustal -sf clustal test.out -osf embl FI test.out FP 1 /^ID ALNM1; .* 120 BP\.\n/ FP 1 /^ID ALNM2; .* 120 BP\.\n/ FP 1 /^ID ALNM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-codata AP seqret CL -auto ../../data/dna.m-codata test.out -osf embl FI test.out FP 1 /^ID C30001; .* 120 BP\.\n/ FP 1 /^ID C30002; .* 120 BP\.\n/ FP 1 /^ID C30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-codata AP seqret CL -auto codata::../../data/dna.m-codata test.out -osf embl FI test.out FP 1 /^ID C30001; .* 120 BP\.\n/ FP 1 /^ID C30002; .* 120 BP\.\n/ FP 1 /^ID C30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-codata AP seqret CL -auto ../../data/dna.m-codata -sf codata test.out -osf embl FI test.out FP 1 /^ID C30001; .* 120 BP\.\n/ FP 1 /^ID C30002; .* 120 BP\.\n/ FP 1 /^ID C30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-embl AP seqret CL -auto ../../data/dna.m-embl test.out -osf embl FI test.out FP 1 /^ID F30001; .* 120 BP\.\n/ FP 1 /^ID F30002; .* 120 BP\.\n/ FP 1 /^ID F30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-embl AP seqret CL -auto embl::../../data/dna.m-embl test.out -osf embl FI test.out FP 1 /^ID F30001; .* 120 BP\.\n/ FP 1 /^ID F30002; .* 120 BP\.\n/ FP 1 /^ID F30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-embl AP seqret CL -auto ../../data/dna.m-embl -sf embl test.out -osf embl FI test.out FP 1 /^ID F30001; .* 120 BP\.\n/ FP 1 /^ID F30002; .* 120 BP\.\n/ FP 1 /^ID F30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-fasta AP seqret CL -auto ../../data/dna.m-fasta test.out -osf embl FI test.out FP 1 /^ID F30001; .* 120 BP\.\n/ FP 1 /^ID F30002; .* 120 BP\.\n/ FP 1 /^ID F30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-fasta AP seqret CL -auto fasta::../../data/dna.m-fasta test.out -osf embl FI test.out FP 1 /^ID F30001; .* 120 BP\.\n/ FP 1 /^ID F30002; .* 120 BP\.\n/ FP 1 /^ID F30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-fasta AP seqret CL -auto ../../data/dna.m-fasta -sf fasta test.out -osf embl FI test.out FP 1 /^ID F30001; .* 120 BP\.\n/ FP 1 /^ID F30002; .* 120 BP\.\n/ FP 1 /^ID F30003; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-fitch AP seqret CL -auto ../../data/dna.fitch test.out -osf embl FI test.out FP 1 /^ID FASTAM1; .* 120 BP\.\n/ FP 1 /^ID FASTAM2; .* 120 BP\.\n/ FP 1 /^ID FASTAM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-fitch AP seqret CL -auto fitch::../../data/dna.fitch test.out -osf embl FI test.out FP 1 /^ID FASTAM1; .* 120 BP\.\n/ FP 1 /^ID FASTAM2; .* 120 BP\.\n/ FP 1 /^ID FASTAM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-fitch AP seqret CL -auto ../../data/dna.fitch -sf fitch test.out -osf embl FI test.out FP 1 /^ID FASTAM1; .* 120 BP\.\n/ FP 1 /^ID FASTAM2; .* 120 BP\.\n/ FP 1 /^ID FASTAM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-mase AP seqret CL -auto mase::../../data/test.mase test.out -osf swiss FI test.out FP 1 /^ID Sequence1 Unreviewed; 120 AA\.\n/ FP 1 /^ID Sequence2 Unreviewed; 120 AA\.\n/ FP 1 /^DE First protein sequence\n/ FP 1 /^SQ SEQUENCE 120 AA; 12728 MW; F55A82D26A16578D CRC64;/ FP 2 /^ID/ // ID seq-inmulti-mase AP seqret CL -auto ../../data/test.mase -sf mase test.out -osf swiss FI test.out FP 1 /^ID Sequence1 Unreviewed; 120 AA\.\n/ FP 1 /^ID Sequence2 Unreviewed; 120 AA\.\n/ FP 1 /^DE First protein sequence\n/ FP 1 /^SQ SEQUENCE 120 AA; 12728 MW; F55A82D26A16578D CRC64;/ FP 2 /^ID/ // ID seq-inmultiauto-msf AP seqret CL -auto ../../data/dna.msf test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-msf AP seqret CL -auto msf::../../data/dna.msf test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-msf AP seqret CL -auto ../../data/dna.msf -sf msf test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-msf8 AP seqret CL -auto ../../data/dna.msf8 test.out -osf embl FI test.out FP 1 /^ID fastam1; .* 121 BP\.\n/ FP 1 /^ID fastam2; .* 121 BP\.\n/ FP 1 /^ID fastam3; .* 121 BP\.\n/ FP 2 /^SQ Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/ FP 1 /^SQ Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/ // ID seq-inmultiusa-msf8 AP seqret CL -auto msf::../../data/dna.msf8 test.out -osf embl FI test.out FP 1 /^ID fastam1; [^\n]* 121 BP\.\n/ FP 1 /^ID fastam2; [^\n]* 121 BP\.\n/ FP 1 /^ID fastam3; [^\n]* 121 BP\.\n/ FP 2 /^SQ Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/ FP 1 /^SQ Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/ // ID seq-inmulti-msf8 AP seqret CL -auto ../../data/dna.msf8 -sf msf test.out -osf embl FI test.out FP 1 /^ID fastam1; .* 121 BP\.\n/ FP 1 /^ID fastam2; .* 121 BP\.\n/ FP 1 /^ID fastam3; .* 121 BP\.\n/ FP 2 /^SQ Sequence 121 BP; 30 A; 30 C; 30 G; 30 T; 1 other;/ FP 1 /^SQ Sequence 121 BP; 29 A; 29 C; 29 G; 29 T; 5 other;/ // ID seq-inmultiauto-ncbi AP seqret CL -auto ../../data/dna.m-ncbi test.out -osf embl FI test.out FP 1 /^ID N30001; .* 144 BP\.\n/ FP 1 /^ID N30002; .* 144 BP\.\n/ FP 1 /^ID N30003; .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seq-inmultiusa-ncbi AP seqret CL -auto ncbi::../../data/dna.m-ncbi test.out -osf embl FI test.out FP 1 /^ID N30001; .* 144 BP\.\n/ FP 1 /^ID N30002; .* 144 BP\.\n/ FP 1 /^ID N30003; .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seq-inmulti-ncbi AP seqret CL -auto ../../data/dna.m-ncbi -sf ncbi test.out -osf embl FI test.out FP 1 /^ID N30001; .* 144 BP\.\n/ FP 1 /^ID N30002; .* 144 BP\.\n/ FP 1 /^ID N30003; .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seq-in-phylip AP seqret CL -auto ../../data/dna.phylip -sf phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inauto-phylip AP seqret CL -auto ../../data/dna.phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-phylip AP seqret CL -auto ../../data/dna.phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-phylip AP seqret CL -auto phylip::../../data/dna.phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-phylip AP seqret CL -auto ../../data/dna.phylip -sf phylip test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiauto-phylipnon AP seqret CL -auto ../../data/dna.phylip3 test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-phylipnon AP seqret CL -auto phylipnon::../../data/dna.phylip3 test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmulti-phylipnon AP seqret CL -auto ../../data/dna.phylip3 -sf phylipnon test.out -osf embl FI test.out FP 1 /^ID MSFM1; .* 120 BP\.\n/ FP 1 /^ID MSFM2; .* 120 BP\.\n/ FP 1 /^ID MSFM3; .* 120 BP\.\n/ FP 2 /^SQ Sequence 120 BP; 30 A; 30 C; 30 G; 30 T; 0 other;/ FP 1 /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;/ // ID seq-inmultiusa-stockholm AP seqret CL -auto stockholm::../../data/PF00032_seed.sth test.out -osf swiss FI test.out FZ = 2304 FP 9 /^ID/ FP /^ID PETD_SYNP2\/65-160 Reviewed; 116 AA\.\n/ FP /^SQ SEQUENCE 116 AA; 12467 MW; B077FB597F735C49 CRC64;/ // ID seq-inmulti-stockholm AP seqret CL -auto ../../data/PF00032_seed.sth -sf stockholm test.out -osf swiss FI test.out FZ = 2304 FP 9 /^ID/ FP /^ID PETD_SYNP2\/65-160 Reviewed; 116 AA\.\n/ FP /^SQ SEQUENCE 116 AA; 12467 MW; B077FB597F735C49 CRC64;/ // ID seq-inmultiusa-stockholm2 AP seqret CL -auto stockholm::../../data/PF00032_seed.pfam2 test.out -osf swiss FI test.out FZ = 2304 FP 9 /^ID/ FP /^ID PETD_SYNP2\/65-160 Reviewed; 116 AA\.\n/ FP /^SQ SEQUENCE 116 AA; 12467 MW; B077FB597F735C49 CRC64;/ // ID seq-inmulti-stockholm2 AP seqret CL -auto ../../data/PF00032_seed.pfam2 -sf stockholm test.out -osf swiss FI test.out FZ = 2304 FP 9 /^ID/ FP /^ID PETD_SYNP2\/65-160 Reviewed; 116 AA\.\n/ FP /^SQ SEQUENCE 116 AA; 12467 MW; B077FB597F735C49 CRC64;/ // ID seq-inmultiusa-stockholm3 AP seqret CL -auto stockholm::../../data/PF00032_seed.pfam3 test.out -osf swiss FI test.out FZ = 2304 FP 9 /^ID/ FP /^ID PETD_SYNP2\/65-160 Reviewed; 116 AA\.\n/ FP /^SQ SEQUENCE 116 AA; 12467 MW; B077FB597F735C49 CRC64;/ // ID seq-inmulti-stockholm3 AP seqret CL -auto ../../data/PF00032_seed.pfam3 -sf stockholm test.out -osf swiss FI test.out FZ = 2304 FP 9 /^ID/ FP /^ID PETD_SYNP2\/65-160 Reviewed; 116 AA\.\n/ FP /^SQ SEQUENCE 116 AA; 12467 MW; B077FB597F735C49 CRC64;/ // ID seq-inmultiusa-stockholmdos AP seqret CL -auto stockholm::../../data/dosfile.sth test.out -osf swiss FI test.out FZ = 1234 FP 8 /^ID/ FP /^ID YA80_HAEIN Reviewed; 30 AA\.\n/ FP /^SQ SEQUENCE 30 AA; 2175 MW; 3B8F297C2C1E4614 CRC64;/ // ID seq-inmulti-stockholmdos AP seqret CL -auto ../../data/dosfile.sth -sf stockholm test.out -osf swiss FI test.out FZ = 1234 FP 8 /^ID/ FP /^ID YA80_HAEIN Reviewed; 30 AA\.\n/ FP /^SQ SEQUENCE 30 AA; 2175 MW; 3B8F297C2C1E4614 CRC64;/ // ID seq-inmultiauto-strider AP seqret CL -auto ../../data/dna.m-strider test.out -osf embl FI test.out FP 1 /^ID STRIDERM1; .* 144 BP\.\n/ FP 1 /^ID STRIDERM2; .* 144 BP\.\n/ FP 1 /^ID STRIDERM3; .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seq-inmultiusa-strider AP seqret CL -auto strider::../../data/dna.m-strider test.out -osf embl FI test.out FP 1 /^ID STRIDERM1; .* 144 BP\.\n/ FP 1 /^ID STRIDERM2; .* 144 BP\.\n/ FP 1 /^ID STRIDERM3; .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seq-inmulti-strider AP seqret CL -auto ../../data/dna.m-strider -sf strider test.out -osf embl FI test.out FP 1 /^ID STRIDERM1; .* 144 BP\.\n/ FP 1 /^ID STRIDERM2; .* 144 BP\.\n/ FP 1 /^ID STRIDERM3; .* 144 BP\.\n/ FP 3 /Sequence 144 BP; 36 A; 36 C; 36 G; 36 T; 0 other;/ // ID seq-inauto-nonewline AP seqret CL -auto ../../data/dna.nonewline test.out -osf embl FI test.out FP /^ID .* 48 BP\.\n/ FP /^SQ Sequence 48 BP; 10 A; 10 C; 10 G; 10 T; 8 other;/ // ID seq-inauto-empty AP seqret CL -auto stdin test.out -osf embl ER 1 FI stderr FZ = 109 FP /Error: Unable to read sequence 'stdin'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seq-in-badformat ## ## bad format name - but still reads (auto) it if it can ## AP seqret CL -auto ../../data/dna.fasta -sf badformat test.out -osf embl FI stderr FP /Unknown input format 'badformat'/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP /^ID .* 100 BP\.\n/ FP /SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-in-badusaformat ## ## bad format name - but still reads (auto) it if it can ## AP seqret CL -auto badformat::../../data/dna.fasta test.out -osf embl FI stderr FP /Unknown input format 'badformat'/ FP 0 /Warning: / FP 1 /Error: / FP 0 /Died: / FI test.out FP /^ID .* 100 BP\.\n/ FP /SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;/ // ID seq-outusa-acedb AP seqret CL -auto ../../data/dna.embl acedb::test.out FI test.out FZ = 116 FP /^DNA : "EMBL"\n/ // ID seq-out-acedb AP seqret CL -auto ../../data/dna.embl test.out -osf acedb FI test.out FZ = 116 FP /^DNA : "EMBL"\n/ // ID seq-outusa-asn1 AP seqret CL -auto ../../data/dna.embl asn1::test.out FI test.out FZ = 291 FP /repr raw, mol dna, length 100, topology linear,/ FP /id \{ local id 1 \},/ // ID seq-out-asn1 AP seqret CL -auto ../../data/dna.embl test.out -osf asn1 FI test.out FZ = 291 FP /repr raw, mol dna, length 100, topology linear,/ FP /id \{ local id 1 \},/ // ID seq-outusa-codata AP seqret CL -auto ../../data/dna.embl codata::test.out FI test.out FZ = 419 FP /^ 61 a c g t a c g t a c g t a c g t a c g t a c g t a c g t a c\n/ FP /^ENTRY EMBL/ FP /^TITLE EMBL FORMAT DNA SEQUENCE, 100 bases/ FP /^ACCESSION E10002/ FP /^\/\/\/\n/ // ID seq-out-codata AP seqret CL -auto ../../data/dna.embl test.out -osf codata FI test.out FZ = 419 FP /^ 61 a c g t a c g t a c g t a c g t a c g t a c g t a c g t a c\n/ FP /^ENTRY EMBL/ FP /^TITLE EMBL FORMAT DNA SEQUENCE, 100 bases/ FP /^ACCESSION E10002/ FP /^\/\/\/\n/ // ID seq-outusa-debug AP seqret CL -auto ../../data/dna.embl debug::test.out FI test.out FZ = 1125 FP /^ Name: 'EMBL'\n/ FP /^ Accession: 'E10002'\n/ FP /^ SeqVersion: 'E10002\.34'\n/ FP /^ GenInfo Id: ''\n/ FP /^ Description: 'EMBL FORMAT DNA SEQUENCE'\n/ FP /^ Keywordlist: \(2\)\n/ FP /^ 'DNA binding protein'\n/ FP /^ 'repressor'\n/ FP /^ Taxonomy: 'Escherichia coli'\n/ FP /^ Taxlist: \(5\)\n/ FP /^ 'Bacteria'\n/ FP /^ 'Proteobacteria'\n/ FP /^ 'gamma subdivision'\n/ FP /^ 'Enterobacteriaceae'\n/ FP /^ 'Escherichia'\n/ FP /^ Type: 'N'\n/ FP /^ Usa: 'debug::test\.out'\n/ FP /^ Input format: 'embl'\n/ FP /^ Ufo: ''\n/ FP /^ Entryname: 'EMBL'\n/ FP /^ File name: 'test\.out'\n/ FP /^ Extension: 'fasta'\n/ FP /^ Single: 'No'\n/ FP /^ Features: 'No'\n/ FP /^ Count: '0'\n/ FP /^ 51 gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 100\n/ // ID seq-out-debug AP seqret CL -auto ../../data/dna.embl test.out -osf debug FI test.out FZ = 1118 FP /^ Name: 'EMBL'\n/ FP /^ Accession: 'E10002'\n/ FP /^ SeqVersion: 'E10002\.34'\n/ FP /^ GenInfo Id: ''\n/ FP /^ Description: 'EMBL FORMAT DNA SEQUENCE'\n/ FP /^ Keywordlist: \(2\)\n/ FP /^ 'DNA binding protein'\n/ FP /^ 'repressor'\n/ FP /^ Taxonomy: 'Escherichia coli'\n/ FP /^ Taxlist: \(5\)\n/ FP /^ 'Bacteria'\n/ FP /^ 'Proteobacteria'\n/ FP /^ 'gamma subdivision'\n/ FP /^ 'Enterobacteriaceae'\n/ FP /^ 'Escherichia'\n/ FP /^ Type: 'N'\n/ FP /^ Usa: 'test\.out'\n/ FP /^ Input format: 'embl'\n/ FP /^ Ufo: ''\n/ FP /^ Entryname: 'EMBL'\n/ FP /^ File name: 'test\.out'\n/ FP /^ Extension: 'debug'\n/ FP /^ Single: 'No'\n/ FP /^ Features: 'No'\n/ FP /^ Count: '0'\n/ FP /^ 51 gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 100\n/ // ID seq-outusa-embl AP seqret CL -auto ../../data/dna.embl embl::test.out FI test.out FZ = 487 FP /^ID E10002; SV 34; linear; unassigned DNA; STD; UNC; 100 BP\.\n/ FP /^AC E10002;\n/ FP /^DE EMBL FORMAT DNA SEQUENCE\n/ FP /^KW DNA binding protein; repressor\.\n/ FP /^OS Escherichia coli\n/ FP /^OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^OC Escherichia\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 60\n/ // ID seq-out-embl AP seqret CL -auto ../../data/dna.embl test.out -osf embl FI test.out FZ = 487 FP /^ID E10002; SV 34; linear; unassigned DNA; STD; UNC; 100 BP\.\n/ FP /^AC E10002;\n/ FP /^DE EMBL FORMAT DNA SEQUENCE\n/ FP /^KW DNA binding protein; repressor\.\n/ FP /^OS Escherichia coli\n/ FP /^OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^OC Escherichia\.\n/ FP /^SQ Sequence 100 BP; 25 A; 25 C; 25 G; 25 T; 0 other;\n/ FP /^ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt 60\n/ // ID seq-outusa-experiment AP seqret CL -auto ../../data/dna.embl experiment::test.out FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^\s+ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\s+100\n/ // ID seq-out-experiment AP seqret CL -auto ../../data/dna.embl test.out -osf experiment FI test.out FZ = 469 FP /^ID EMBL standard; DNA; UNC; 100 BP\.\n/ FP /^\s+ acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\s+100\n/ // ID seq-outusa-fasta AP seqret CL -auto ../../data/dna.embl fasta::test.out FI test.out FZ = 143 FP /^>EMBL E10002\.34 EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-out-fasta AP seqret CL -auto ../../data/dna.embl test.out -osf fasta FI test.out FZ = 143 FP /^>EMBL E10002\.34 EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-outusa-fitch AP seqret CL -auto ../../data/dna.embl fitch::test.out FI test.out FZ = 152 FP /^EMBL, 100 bases\n/ FP /^ acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt\n/ // ID seq-out-fitch AP seqret CL -auto ../../data/dna.embl test.out -osf fitch FI test.out FZ = 152 FP /^EMBL, 100 bases\n/ FP /^ acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt acg tac gta cgt\n/ // ID seq-outusa-gcg AP seqret CL -auto ../../data/dna.embl gcg::test.out FI test.out FZ = 211 FP /^\!\!NA_SEQUENCE 1\.0\n/ FP /^EMBL Length: 100 Type: N Check: 6856 \.\.\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac\n/ // ID seq-out-gcg AP seqret CL -auto ../../data/dna.embl test.out -osf gcg FI test.out FZ = 211 FP /^\!\!NA_SEQUENCE 1\.0\n/ FP /^EMBL Length: 100 Type: N Check: 6856 \.\.\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac\n/ // ID seq-outusa-genbank AP seqret CL -auto ../../data/dna.embl genbank::test.out FI test.out FZ = 503 FP /^LOCUS EMBL 100 bp DNA linear UNC \d\d-[A-Z][A-Z][A-Z]-20[0-9][0-9]\n/ FP /^DEFINITION EMBL FORMAT DNA SEQUENCE\.\n/ FP /^ACCESSION E10002\n/ FP /^VERSION E10002\.34\n/ FP /^KEYWORDS DNA binding protein; repressor\.\n/ FP /^SOURCE Escherichia coli\n/ FP /^ ORGANISM Escherichia coli\n/ FP /^ Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^ Escherichia\.\n/ FP /^ORIGIN\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\n/ // ID seq-out-genbank AP seqret CL -auto ../../data/dna.embl test.out -osf genbank FI test.out FZ = 503 FP /^LOCUS EMBL 100 bp DNA linear UNC \d\d-[A-Z][A-Z][A-Z]-20[0-9][0-9]\n/ FP /^DEFINITION EMBL FORMAT DNA SEQUENCE\.\n/ FP /^ACCESSION E10002\n/ FP /^VERSION E10002\.34\n/ FP /^KEYWORDS DNA binding protein; repressor\.\n/ FP /^SOURCE Escherichia coli\n/ FP /^ ORGANISM Escherichia coli\n/ FP /^ Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;\n/ FP /^ Escherichia\.\n/ FP /^ORIGIN\n/ FP /^ 1 acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt acgtacgtac gtacgtacgt\n/ // ID seq-outusa-gff AP seqret CL -auto ../../data/dna.embl gff::test.out FI test.out FZ = 257 FP /^##gff-version 3\n/ FP /^##sequence-region EMBL 1 100\n/ FP /^#\!Source-version EMBOSS [0-9\.]+\n/ FP /^#\!Date [0-9\-]+\n/ FP /^#\!Type DNA\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-out-gff AP seqret CL -auto ../../data/dna.embl test.out -osf gff FI test.out FZ = 257 FP /^##gff-version 3\n/ FP /^##sequence-region EMBL 1 100\n/ FP /^#\!Source-version EMBOSS [0-9\.]+\n/ FP /^#\!Date [0-9\-]+\n/ FP /^#\!Type DNA\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-outusa-ig AP seqret CL -auto ../../data/dna.embl ig::test.out FI test.out FZ = 145 FP /;EMBL FORMAT DNA SEQUENCE, 100 bases\n/ FP /EMBL\n/ FP /gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt1\n/ // ID seq-out-ig AP seqret CL -auto ../../data/dna.embl test.out -osf ig FI test.out FZ = 145 FP /;EMBL FORMAT DNA SEQUENCE, 100 bases\n/ FP /EMBL\n/ FP /gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt1\n/ // ID seq-outusa-ncbi AP seqret CL -auto ../../data/dna.embl ncbi::test.out FI test.out FZ = 153 FP /^>gnl\|unk\|EMBL \(E10002\.34\) EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-out-ncbi AP seqret CL -auto ../../data/dna.embl test.out -osf ncbi FI test.out FZ = 153 FP /^>gnl\|unk\|EMBL \(E10002\.34\) EMBL FORMAT DNA SEQUENCE\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-outusa-staden AP seqret CL -auto ../../data/dna.embl staden::test.out FI test.out FZ = 113 FP // FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-out-staden AP seqret CL -auto ../../data/dna.embl test.out -osf staden FI test.out FZ = 113 FP // FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-outusa-strider AP seqret CL -auto ../../data/dna.embl strider::test.out FI test.out FZ = 166 FP /^; ### from DNA Strider ;-\)\n/ FP /^; DNA sequence EMBL, 100 bases\n/ FP /^;\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtac\n/ // ID seq-out-strider AP seqret CL -auto ../../data/dna.embl test.out -osf strider FI test.out FZ = 166 FP /^; ### from DNA Strider ;-\)\n/ FP /^; DNA sequence EMBL, 100 bases\n/ FP /^;\n/ FP /^acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtac\n/ // ID seq-outusa-swiss AP seqret CL -auto ../../data/prot.swiss swiss::test.out FI test.out FZ = 288 FP /^ID FASTA Unreviewed; 100 AA\.\n/ FP /^AC S00001;\n/ FP /^DE FASTA FORMAT PROTEIN SEQUENCE\n/ FP /^SQ SEQUENCE 100 AA; 11907 MW; DCEF6AA9E9BA19B4 CRC64;\n/ FP /^ ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/ FP /^ ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/ // ID seq-out-swiss AP seqret CL -auto ../../data/prot.swiss test.out -osf swiss FI test.out FZ = 288 FP /^ID FASTA Unreviewed; 100 AA\.\n/ FP /^AC S00001;\n/ FP /^DE FASTA FORMAT PROTEIN SEQUENCE\n/ FP /^SQ SEQUENCE 100 AA; 11907 MW; DCEF6AA9E9BA19B4 CRC64;\n/ FP /^ ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/ FP /^ ACDEFGHIKL MNPQRSTVWY ACDEFGHIKL MNPQRSTVWY\n/ // ID seq-outusa-text AP seqret CL -auto ../../data/dna.embl text::test.out FI test.out FZ = 102 FP /^gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-out-text AP seqret CL -auto ../../data/dna.embl test.out -osf text FI test.out FZ = 102 FP /^gtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgt\n/ // ID seq-outmultiusa-acedb AP seqret CL -auto ../../data/dna.m-embl acedb::test.out FI test.out FZ = 420 FP 3 /^DNA : "FASTAM[1-3]"/ // ID seq-outmulti-acedb AP seqret CL -auto ../../data/dna.m-embl test.out -osf acedb FI test.out FZ = 420 FP 3 /^DNA : "FASTAM[1-3]"/ // ID seq-outmultiusa-asn1 AP seqret CL -auto ../../data/dna.m-embl asn1::test.out FI test.out FZ = 957 FP 3 /^ id \{ local id 1 \},/ FP 3 /^ descr { title "FASTA FORMAT DNA SEQUENCE F3000[1-3]" },\n/ FP /^ descr { title "FASTA FORMAT DNA SEQUENCE F30003" },\n/ // ID seq-outmulti-asn1 AP seqret CL -auto ../../data/dna.m-embl test.out -osf asn1 FI test.out FZ = 957 FP 3 /^ id \{ local id 1 \},/ FP 3 /^ descr { title "FASTA FORMAT DNA SEQUENCE F3000[1-3]" },\n/ FP /^ descr { title "FASTA FORMAT DNA SEQUENCE F30003" },\n/ // ID seq-outmultiusa-clustal AP seqret CL -auto ../../data/dna.m-embl clustal::test.out FI test.out FZ = 664 FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/ FP /^FASTAM2 ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-outmulti-clustal AP seqret CL -auto ../../data/dna.m-embl test.out -osf clustal FI test.out FZ = 664 FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/ FP /^FASTAM2 ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGT\n/ // ID seq-outmultiusa-clustalprot AP seqret CL -auto ../../data/prot.m-swiss clustal::test.out FI test.out FZ = 584 FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/ FP /^SWISSM2 AACCDDEEFFGGHHIIKKLLMMNNPPQQRRSSTTVVWWYYAACCDDEEFFGGHHIIKKLL\n/ FP 3 /^\n/ FP 1 /^ \n/ // ID seq-outmulti-clustalprot AP seqret CL -auto ../../data/prot.m-swiss test.out -osf clustal FI test.out FZ = 584 FP /^CLUSTAL W \(1\.83\) multiple sequence alignment\n/ FP /^SWISSM2 AACCDDEEFFGGHHIIKKLLMMNNPPQQRRSSTTVVWWYYAACCDDEEFFGGHHIIKKLL\n/ FP 3 /^\n/ FP 1 /^ \n/ // ID seq-outmultiusa-codata AP seqret CL -auto ../../data/dna.m-embl codata::test.out FI test.out FZ = 1410 FP 3 /^ENTRY FASTAM[1-3] \n/ FP 3 /^\/\/\/\n/ // ID seq-outmulti-codata AP seqret CL -auto ../../data/dna.m-embl test.out -osf codata FI test.out FZ = 1410 FP 3 /^ENTRY FASTAM[1-3] \n/ FP 3 /^\/\/\/\n/ // ID seq-outmultiusa-debug AP seqret CL -auto ../../data/dna.m-embl debug::test.out FI test.out FZ = 3003 FP 3 /^ Name: 'FASTAM[1-3]'\n/ FP 3 /^ Accession: 'F3000[1-3]'\n/ FP /^ Entryname: 'FASTAM3'\n/ FP 3 /^ Usa: 'debug::test\.out'\n/ FP 3 /^ Input format: 'embl'\n/ FP 3 /^ Ufo: ''\n/ FP 3 /^ Entryname: 'FASTAM[1-3]'\n/ FP 3 /^ File name: 'test\.out'\n/ FP 3 /^ Extension: 'fasta'\n/ // ID seq-outmulti-debug AP seqret CL -auto ../../data/dna.m-embl test.out -osf debug FI test.out FZ = 2982 FP 3 /^ Name: 'FASTAM[1-3]'\n/ FP 3 /^ Accession: 'F3000[1-3]'\n/ FP /^ Entryname: 'FASTAM3'\n/ FP 3 /^ Usa: 'test\.out'\n/ FP 3 /^ Input format: 'embl'\n/ FP 3 /^ Ufo: ''\n/ FP 3 /^ Entryname: 'FASTAM[1-3]'\n/ FP 3 /^ File name: 'test\.out'\n/ FP 3 /^ Extension: 'debug'\n/ // ID seq-outmultiusa-embl AP seqret CL -auto ../../data/dna.m-embl embl::test.out FI test.out FZ = 1023 FP 3 /^ID F3000[1-3]; SV 1; linear; unassigned DNA; STD; UNC; 120 BP\.\n/ FP 3 /^AC F3000[1-3];\n/ FP /^AC F30003;\n/ FP /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;\n/ // ID seq-outmulti-embl AP seqret CL -auto ../../data/dna.m-embl test.out -osf embl FI test.out FZ = 1023 FP 3 /^ID F3000[1-3]; SV 1; linear; unassigned DNA; STD; UNC; 120 BP\.\n/ FP 3 /^AC F3000[1-3];\n/ FP /^AC F30003;\n/ FP /^SQ Sequence 120 BP; 29 A; 29 C; 29 G; 29 T; 4 other;\n/ // ID seq-outmultiusa-fasta AP seqret CL -auto ../../data/dna.m-embl fasta::test.out FI test.out FZ = 513 FP 3 /^>FASTAM[1-3] F3000[1-3] FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>FASTAM3 F30003 FASTA FORMAT DNA SEQUENCE F30003\n/ // ID seq-outmulti-fasta AP seqret CL -auto ../../data/dna.m-embl test.out -osf fasta FI test.out FZ = 513 FP 3 /^>FASTAM[1-3] F3000[1-3] FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>FASTAM3 F30003 FASTA FORMAT DNA SEQUENCE F30003\n/ // ID seq-outmultiusa-fitch AP seqret CL -auto ../../data/dna.m-embl fitch::test.out FI test.out FZ = 543 FP 3 /^FASTAM[1-3], 120 bases\n/ FP /^FASTAM1, 120 bases\n/ FP /^ ACG TAC GTA CGT ACG TAC GT- --- ACG TAC GTA CGT ACG TAC GTA CGT ACG TAC GTA CGT\n/ // ID seq-outmulti-fitch AP seqret CL -auto ../../data/dna.m-embl test.out -osf fitch FI test.out FZ = 543 FP 3 /^FASTAM[1-3], 120 bases\n/ FP /^FASTAM1, 120 bases\n/ FP /^ ACG TAC GTA CGT ACG TAC GT- --- ACG TAC GTA CGT ACG TAC GTA CGT ACG TAC GTA CGT\n/ // ID seq-outmultiusa-gcg AP seqret CL -auto ../../data/dna.m-embl gcg::test.out FI test.out FZ = 750 FP 3 /^!!NA_SEQUENCE 1\.0\n/ FP /^FASTAM1 Length: 120 Type: N Check: 8587 \.\.\n/ FP /^FASTAM2 Length: 120 Type: N Check: 6178 \.\.\n/ FP /^FASTAM3 Length: 120 Type: N Check: 8431 \.\.\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ // ID seq-outmulti-gcg AP seqret CL -auto ../../data/dna.m-embl test.out -osf gcg FI test.out FZ = 750 FP 3 /^!!NA_SEQUENCE 1\.0\n/ FP /^FASTAM1 Length: 120 Type: N Check: 8587 \.\.\n/ FP /^FASTAM2 Length: 120 Type: N Check: 6178 \.\.\n/ FP /^FASTAM3 Length: 120 Type: N Check: 8431 \.\.\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ // ID seq-outmultiusa-genbank AP seqret CL -auto ../../data/dna.m-embl genbank::test.out FI test.out FZ = 921 FP 3 /^LOCUS FASTAM[1-3] / FP /^LOCUS FASTAM3 / FP 3 /^ACCESSION F3000[1-3]\n/ FP /^ACCESSION F30003\n/ FP 3 /^\/\/\n/ // ID seq-outmulti-genbank AP seqret CL -auto ../../data/dna.m-embl test.out -osf genbank FI test.out FZ = 921 FP 3 /^LOCUS FASTAM[1-3] / FP /^LOCUS FASTAM3 / FP 3 /^ACCESSION F3000[1-3]\n/ FP /^ACCESSION F30003\n/ FP 3 /^\/\/\n/ // ID seq-outmultiusa-gff AP seqret CL -auto ../../data/dna.m-embl gff::test.out FI test.out FZ = 864 FP 3 /^##sequence-region FASTAM[1-3] 1 120\n/ FP 3 /^#\!Type DNA\n/ FP /^##sequence-region FASTAM2 1 120\n/ FP 3 /^##FASTA\n/ // ID seq-outmulti-gff AP seqret CL -auto ../../data/dna.m-embl test.out -osf gff FI test.out FZ = 864 FP 3 /^##sequence-region FASTAM[1-3] 1 120\n/ FP 3 /^#\!Type DNA\n/ FP /^##sequence-region FASTAM2 1 120\n/ FP 3 /^##FASTA\n/ // ID seq-outmultiusa-gffprot AP seqret CL -auto ../../data/prot.m-swiss gff::test.out FI test.out FZ = 765 FP 3 /^#!Type Protein\n/ FP 3 /^##sequence-region SWISSM[1-3] 1 \d+\n/ FP 1 /^##sequence-region SWISSM2 1 80\n/ FP 3 /^#!Type Protein\n/ // ID seq-outmulti-gffprot AP seqret CL -auto ../../data/prot.m-swiss test.out -osf gff FI test.out FZ = 765 FP 3 /^#!Type Protein\n/ FP 3 /^##sequence-region SWISSM[1-3] 1 \d+\n/ FP 1 /^##sequence-region SWISSM2 1 80\n/ FP 3 /^#!Type Protein\n/ // ID seq-outmultiusa-hennig86 AP seqret CL -auto ../../data/dna.m-embl hennig86::test.out FI test.out FZ = 432 FP /^xread\n/ FP /^' Written by EMBOSS [0-9][0-9]\/[01][0-9]\/[0-9][0-9] '\n/ FP /^120 3\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^03210321032103210321\?\?\?\?032103210321032103210321032103210321032103210321032103210321032103210321032103210321123003210321\n/ FP /^;\n/ // ID seq-outmulti-hennig86 AP seqret CL -auto ../../data/dna.m-embl test.out -osf hennig86 FI test.out FZ = 432 FP /^xread\n/ FP /^' Written by EMBOSS [0-9][0-9]\/[01][0-9]\/[0-9][0-9] '\n/ FP /^120 3\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^03210321032103210321\?\?\?\?032103210321032103210321032103210321032103210321032103210321032103210321032103210321123003210321\n/ FP /^;\n/ // ID seq-outmultiusa-jackknifer AP seqret CL -auto ../../data/dna.m-embl jackknifer::test.out FI test.out FZ = 590 FP /^' Written by EMBOSS [0-9\/]+ \n/ FP 3 /^\(FASTAM3\) [ACGT.\-]+\n/ // ID seq-outmulti-jackknifer AP seqret CL -auto ../../data/dna.m-embl test.out -osf jackknifer FI test.out FZ = 590 FP /^' Written by EMBOSS [0-9\/]+ \n/ FP 3 /^\(FASTAM3\) [ACGT.\-]+\n/ // ID seq-outmultiusa-mega AP seqret CL -auto ../../data/dna.m-embl mega::test.out FI test.out FZ = 722 FP /^#mega\n/ FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/ FP 9 /^#FASTAM[1-3] [ACGT.\-]+\n/ FP 7 /^\n/ // ID seq-outmulti-mega AP seqret CL -auto ../../data/dna.m-embl test.out -osf mega FI test.out FZ = 722 FP /^#mega\n/ FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/ FP 9 /^#FASTAM[1-3] [ACGT.\-]+\n/ FP 7 /^\n/ // ID seq-outmultiusa-meganon AP seqret CL -auto ../../data/dna.m-embl meganon::test.out FI test.out FZ = 633 FP /^#mega\n/ FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/ FP /^#FASTAM2\n/ FP 3 /^#FASTAM[1-3]\n/ // ID seq-outmulti-meganon AP seqret CL -auto ../../data/dna.m-embl test.out -osf meganon FI test.out FZ = 633 FP /^#mega\n/ FP /^[!]Title: Written by EMBOSS [0-9\/]+;\n/ FP /^#FASTAM2\n/ FP 3 /^#FASTAM[1-3]\n/ // ID seq-outmultiusa-msf AP seqret CL -auto ../../data/dna.m-embl msf::test.out FI test.out FZ = 880 FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 120 Type: N [0-9\/]+ CompCheck: 3196 \.\.\n/ FP /^ Name: FASTAM1 Len: 120 Check: 8587 Weight: 1\.00\n/ FP /^ Name: FASTAM2 Len: 120 Check: 6178 Weight: 1\.00\n/ FP /^ Name: FASTAM3 Len: 120 Check: 8431 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 3 /^FASTAM3 [ACGT\-]+\n/ // ID seq-outmulti-msf AP seqret CL -auto ../../data/dna.m-embl test.out -osf msf FI test.out FZ = 880 FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 120 Type: N [0-9\/]+ CompCheck: 3196 \.\.\n/ FP /^ Name: FASTAM1 Len: 120 Check: 8587 Weight: 1\.00\n/ FP /^ Name: FASTAM2 Len: 120 Check: 6178 Weight: 1\.00\n/ FP /^ Name: FASTAM3 Len: 120 Check: 8431 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 3 /^FASTAM3 [ACGT\-]+\n/ // ID seq-outmulti-msf-noalign AP seqret CL -auto "tembl:M1190*" test.out -osf msf FI test.out FZ = 3884 FP /^!!NA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 724 Type: N [0-9/]+ CompCheck: 3521 \.\.\n/ FP 3 /^ Name: M1190/ FP /^ 1 50\n/ FP 11 /^M11904 +[ACGTacgt\-]+\n/ FP 1 /^M11904 +[ACGTacgt\-]+[~]+\n/ FP 3 /^M11904 +[~]+\n/ // ID seq-outmultiusa-msfprot AP seqret CL -auto ../../data/prot.m-swiss msf::test.out FI test.out FZ = 752 FP /^!!AA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 100 Type: P [0-9\/]+ CompCheck: 4147 \.\.\n/ FP /^ Name: SWISSM1 Len: 100 Check: 1414 Weight: 1\.00\n/ FP /^ Name: SWISSM2 Len: 100 Check: 1993 Weight: 1\.00\n/ FP /^ Name: SWISSM3 Len: 100 Check: 740 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 2 /^SWISSM2 [A-Z~]+\n/ // ID seq-outmulti-msfprot AP seqret CL -auto ../../data/prot.m-swiss test.out -osf msf FI test.out FZ = 752 FP /^!!AA_MULTIPLE_ALIGNMENT 1\.0\n/ FP /^ test\.out MSF: 100 Type: P [0-9\/]+ CompCheck: 4147 \.\.\n/ FP /^ Name: SWISSM1 Len: 100 Check: 1414 Weight: 1\.00\n/ FP /^ Name: SWISSM2 Len: 100 Check: 1993 Weight: 1\.00\n/ FP /^ Name: SWISSM3 Len: 100 Check: 740 Weight: 1\.00\n/ FP /^\/\/\n/ FP /^ 1 50\n/ FP 2 /^SWISSM2 [A-Z~]+\n/ // ID seq-outmultiusa-nexus AP seqret CL -auto ../../data/dna.m-embl nexus::test.out FI test.out FZ = 756 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format interleave datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ FP 3 /^FASTAM2 [ACGT\-]+\n/ // ID seq-outmulti-nexus AP seqret CL -auto ../../data/dna.m-embl test.out -osf nexus FI test.out FZ = 756 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format interleave datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ FP 3 /^FASTAM2 [ACGT\-]+\n/ // ID seq-outmultiusa-nexusnon AP seqret CL -auto ../../data/dna.m-embl nexusnon::test.out FI test.out FZ = 572 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP 3 /^FASTAM[1-3]\n/ FP 3 /^[ACGT\-]+\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ // ID seq-outmulti-nexusnon AP seqret CL -auto ../../data/dna.m-embl test.out -osf nexusnon FI test.out FZ = 572 FP /^#NEXUS\n/ FP /^[TITLE: Written by EMBOSS [0-9\/]+]\n/ FP /^begin data;\n/ FP /^dimensions ntax=3 nchar=120;\n/ FP /^format datatype=DNA missing=N gap=-;\n/ FP /^matrix\n/ FP 3 /^FASTAM[1-3]\n/ FP 3 /^[ACGT\-]+\n/ FP /^;\n/ FP /^end;\n/ FP /^begin assumptions;\n/ FP /^options deftype=unord;\n/ // ID seq-outmultiusa-phylip AP seqret CL -auto ../../data/dna.m-embl phylip::test.out FI test.out FZ = 495 FP /^ 3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ // ID seq-outmulti-phylip AP seqret CL -auto ../../data/dna.m-embl test.out -osf phylip FI test.out FZ = 495 FP /^ 3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ // ID seq-outmultiusa-phylipnon AP seqret CL -auto ../../data/dna.m-embl phylipnon::test.out FI test.out FZ = 492 FP /^3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ FP / GTACGTACGT\nFASTAM2/ // ID seq-outmulti-phylipnon AP seqret CL -auto ../../data/dna.m-embl test.out -osf phylipnon FI test.out FZ = 492 FP /^3 120\n/ FP /^FASTAM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC\n/ FP 6 /^ [ACGT \-]+\n/ FP / GTACGTACGT\nFASTAM2/ // ID seq-outmultiusa-swiss AP seqret CL -auto ../../data/prot.m-swiss swiss::test.out FI test.out FZ = 810 FP 3 /^ID SWISSM[1-3] +Unreviewed; +[0-9]+ AA\.\n/ FP /^ID SWISSM2 Unreviewed; 80 AA\.\n/ FP /^SQ SEQUENCE 60 AA; 7151 MW; FF73258FFC19CF5B CRC64;/ FP 3 /^\/\/\n/ // ID seq-outmulti-swiss AP seqret CL -auto ../../data/prot.m-swiss test.out -osf swiss FI test.out FZ = 810 FP 3 /^ID SWISSM[1-3] +Unreviewed; +[0-9]+ AA\.\n/ FP /^ID SWISSM2 Unreviewed; 80 AA\.\n/ FP /^SQ SEQUENCE 60 AA; 7151 MW; FF73258FFC19CF5B CRC64;/ FP 3 /^\/\/\n/ // ID seq-outmultiusa-ncbi AP seqret CL -auto ../../data/dna.m-embl ncbi::test.out FI test.out FZ = 543 FP 3 /^>gnl\|unk\|FASTAM[1-3] \(F3000[1-3]\) FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>gnl\|unk\|FASTAM2 \(F30002\) FASTA FORMAT DNA SEQUENCE F30002\n/ // ID seq-outmulti-ncbi AP seqret CL -auto ../../data/dna.m-embl test.out -osf ncbi FI test.out FZ = 543 FP 3 /^>gnl\|unk\|FASTAM[1-3] \(F3000[1-3]\) FASTA FORMAT DNA SEQUENCE F3000[1-3]\n/ FP /^>gnl\|unk\|FASTAM2 \(F30002\) FASTA FORMAT DNA SEQUENCE F30002\n/ // ID seq-outmultiusa-nbrf AP seqret CL -auto ../../data/dna.m-embl nbrf::test.out FI test.out FZ = 579 FP 3 /^>D1;FASTAM[1-3]\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTA FORMAT DNA SEQUENCE F30001, 120 bases\n/ FP /^ ACGTACGTTG CAACGTACGT\*\n/ // ID seq-outmulti-nbrf AP seqret CL -auto ../../data/dna.m-embl test.out -osf nbrf FI test.out FZ = 579 FP 3 /^>D1;FASTAM[1-3]\n/ FP 3 /^FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTA FORMAT DNA SEQUENCE F30001, 120 bases\n/ FP /^ ACGTACGTTG CAACGTACGT\*\n/ // ID seq-outmultiusa-ig AP seqret CL -auto ../../data/dna.m-embl ig::test.out FI test.out FZ = 531 FP /^;FASTA FORMAT DNA SEQUENCE F30002, 120 bases\n/ FP 3 /^;FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTAM2\n/ FP 3 /^FASTAM[1-3]\n/ FP /^ACGTACGTACGTACGTACGT1\n/ // ID seq-outmulti-ig AP seqret CL -auto ../../data/dna.m-embl test.out -osf ig FI test.out FZ = 531 FP /^;FASTA FORMAT DNA SEQUENCE F30002, 120 bases\n/ FP 3 /^;FASTA FORMAT DNA SEQUENCE F3000[1-3], 120 bases\n/ FP /^FASTAM2\n/ FP 3 /^FASTAM[1-3]\n/ FP /^ACGTACGTACGTACGTACGT1\n/ // ID seq-outmultiusa-strider AP seqret CL -auto ../../data/dna.m-embl strider::test.out FI test.out FZ = 570 FP /^; ### from DNA Strider ;-\)\n/ FP 3 /^; DNA sequence FASTAM[1-3], 120 bases\n/ FP /^; DNA sequence FASTAM2, 120 bases\n/ FP /^;\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-outmulti-strider AP seqret CL -auto ../../data/dna.m-embl test.out -osf strider FI test.out FZ = 570 FP /^; ### from DNA Strider ;-\)\n/ FP 3 /^; DNA sequence FASTAM[1-3], 120 bases\n/ FP /^; DNA sequence FASTAM2, 120 bases\n/ FP /^;\n/ FP /^ACGTACGTACGTACGTACGT\n/ // ID seq-outmultiusa-treecon AP seqret CL -auto ../../data/dna.m-embl treecon::test.out FI test.out FZ = 391 FP /^120\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCAACGTACGT\n/ // ID seq-outmulti-treecon AP seqret CL -auto ../../data/dna.m-embl test.out -osf treecon FI test.out FZ = 391 FP /^120\n/ FP 3 /^FASTAM[1-3]\n/ FP /^FASTAM2\n/ FP /^ACGTACGTACGTACGTACGT----ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTTGCAACGTACGT\n/ // ID seq-offset AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat%1859 FI test.out FZ = 11842 FP /^ID Z46957; / FP /^ID U68037; / FP 5 /^ID/ FI stderr FZ = 0 // ID seq-offset-zero AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat%0 FI test.out FZ = 13320 FP /^ID L48662; / FP /^ID Z46957; / FP /^ID U68037; / FP 6 /^ID/ FI stderr FZ = 0 // ##################################################### # Test the query part of USAs ##################################################### ID seqret-query-direct-fail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:bad:L48662 FI stderr FZ = 583 FP /Error: Unknown query field 'bad' in query '\.\.\/\.\.\/embl\/rod\.dat:bad:L48662'/ FP /Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:bad:L48662'/ FP 0 /Warning: / FP 7 /Error: / FP 1 /Died: / // ID seqret-query-direct-name AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:L48662 FI test.out FZ = 1478 FP /^ID L48662;/ FP 1 /^ID/ // ID seqret-query-direct-name2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:Z46957 FI test.out FZ = 3337 FP /^ID Z46957; / FP 1 /^ID/ // ID seqret-query-direct-namefail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:FAIL FI stderr FZ = 133 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:FAIL'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-id AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:id:L48662 FI test.out FZ = 1478 FP /^ID L48662; / FP 1 /^ID/ // ID seqret-query-direct-id2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ID:Z46957 FI test.out FZ = 3337 FP /^ID Z46957; / FP 1 /^ID/ // ID seqret-query-direct-idfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ID:FAIL FI stderr FZ = 136 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ID:FAIL'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-acc AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:L48662 FI test.out FZ = 1478 FP /^ID L48662; / FP 1 /^ID/ // ID seqret-query-direct-acc2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:Z46957 FI test.out FZ = 3337 FP /^ID Z46957; / FP 1 /^ID/ // ID seqret-query-direct-accfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:Z99999 FI stderr FZ = 139 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ACC:Z99999'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-accfail2 ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ACC:99999Z FI stderr FZ = 139 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ACC:99999Z'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-sv AP seqret CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:SV:L48662*" FI test.out FZ = 1478 FP /^ID L48662; / FP 1 /^ID/ // ID seqret-query-direct-sv2 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:Z46957.1 FI test.out FZ = 3337 FP /^ID Z46957; / FP 1 /^ID/ // ID seqret-query-direct-svfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:SV:Z99999.1 FI stderr FZ = 140 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:SV:Z99999\.1'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-des AP seqret CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:DES:*receptor*" FI test.out FZ = 2978 FP /^ID U68037; / FP 1 /^ID/ // ID seqret-query-direct-des2 AP seqret CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:DES:*norvegicus*" FI test.out FZ = 11842 FP /^ID Z46957; / FP 5 /^ID/ // ID seqret-query-direct-desfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:lynam FI stderr FZ = 138 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:DES:lynam'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-deswordstart AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:Mus FI test.out FZ = 1478 FP /^ID L48662; / FP 1 /^ID/ // ID seqret-query-direct-deswordmid AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:mrna FI test.out FZ = 7793 FP /^ID L48662; / FP 3 /^ID/ // ID seqret-query-direct-deswordend AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:DES:receptor FI test.out FZ = 2978 FP /^ID U68037; / FP 1 /^ID/ // ID seqret-query-direct-key AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:KEY:rhodopsin FI test.out FZ = 3337 FP /^ID Z46957; / FP 1 /^ID/ // ID seqret-query-direct-keyfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:KEY:CHAIN FI stderr FZ = 138 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:KEY:CHAIN'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-direct-org AP seqret CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:ORG:Mus*" FI test.out FZ = 1478 FP /^ID L48662; / FP 1 /^ID/ // ID seqret-query-direct-org2 AP seqret CL -auto -out test.out -osf embl "embl::../../embl/rod.dat:ORG:Rattus*" FI test.out FZ = 11842 FP /^ID Z46957; / FP /^ID U68037; / FP 5 /^ID/ // ID seqret-query-direct-org3 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:Rodentia FI test.out FZ = 13320 FP /^ID L48662; / FP /^ID Z46957; / FP /^ID U68037; / FP 6 /^ID/ // ID seqret-query-direct-orgfail ER 1 AP seqret CL -auto -out test.out -osf embl embl::../../embl/rod.dat:ORG:HOMO FI stderr FZ = 137 FP /^Error: Unable to read sequence 'embl::\.\.\/\.\.\/embl\/rod\.dat:ORG:HOMO'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-srs-id CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs-ID:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-acc CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs-ACC:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-sv CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs-SV:AB000095.1 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-name CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrs:AB000095 FI test.out FZ = 3701 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srs-fail CC Requires a local SRS installation RQ srs ER 1 AP seqret CL -auto -out test.out -osf embl qasrs-id:OLD FI stderr FZ = 116 FP /^Error: Unable to read sequence 'qasrs-id:OLD'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-srsfasta-id CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta-ID:AB000095 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-acc CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta-ACC:AB000095 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-sv CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta-SV:AB000095.1 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-name CC Requires a local SRS installation RQ srs AP seqret CL -auto -out test.out -osf embl qasrsfasta:AB000095 FI test.out FZ = 3407 FP /^ID AB000095 / FP 1 /^ID / // ID seqret-query-srsfasta-fail CC Requires a local SRS installation RQ srs ER 1 AP seqret CL -auto -out test.out -osf embl qasrsfasta-id:OLD FI stderr FZ = 121 FP /^Error: Unable to read sequence 'qasrsfasta-id:OLD'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // ID seqret-query-srswww-id AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-ID:AB000095 FI test.out FZ = 4670 FP /^ID AB000095; / FP 1 /^ID / // ID seqret-query-srswww-acc AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-ACC:AB000095 FI test.out FZ = 4670 FP /^ID AB000095; / FP 1 /^ID / // ID seqret-query-srswww-sv AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-SV:AB000095.1 FI test.out FZ = 4670 FP /^ID AB000095; / FP 1 /^ID / // ID seqret-query-srswww-name AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww:AB000095 FI test.out FZ = 4670 FP /^ID AB000095; / FP 1 /^ID / // ID seqret-query-srswww-fail ER 1 AP seqret CC Requires http access to EBI SRS server CL -auto -out test.out -osf embl qasrswww-id:OLD FI stderr FZ = 119 FP /^Error: Unable to read sequence 'qasrswww-id:OLD'/ FP 0 /Warning: / FP 1 /Error: / FP 1 /Died: / // #################################################### # End of query USA tests #################################################### #################################################### # seqret examples for documentation #################################################### ID seqret-ex UC Extract an entry from a database and write it to a file: AP seqret IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ // ID seqret-ex2 UC Display the contents of the sequence on the screen: AP seqret IN tembl:x65923 IN stdout FI stdout FP /X65923/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID seqret-ex3 UC Write the result in GCG format by using the qualifier '-osformat'. AP seqret CL -osf gcg IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.gcg FP /X65923/ // ID seqret-ex4 UC Write the result in GCG format by specifying the format UC in the output USA on the command line. AP seqret CL -outseq gcg::x65923.gcg IN tembl:x65923 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.gcg FP /X65923/ // ID seqret-ex5 UC Write the result in GCG format by specifying the format UC in the output USA at the prompt. AP seqret IN tembl:x65923 IN gcg::x65923.gcg FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.gcg FP /X65923/ // ID seqret-ex6 UC Write the reverse-complement of a sequence: AP seqret CL -srev IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ // ID seqret-ex7 UC Extract the bases between the positions starting at 5 and ending at 25: AP seqret CL -sbegin 5 -send 25 IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ // ID seqret-ex8 UC Extract the bases between the positions starting at 5 UC and ending at 5 bases before the end of the sequence: AP seqret CL -sbegin 5 -send -5 IN tembl:x65923 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.fasta FP /X65923/ // ID seqret-ex9 UC Read all entries in the database 'tembl' that start with 'h' UC and write them to a file: AP seqret IN tembl:h* IN hall.seq FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hall.seq FP /H45989/ // ID seqret-ex10 UC Read all entries in the database 'tembl' that start with 'ab' UC and write them to a file. UC In this example the specification is all done in the command line UC and to stop Unix getting confused by the '*' character, UC it has to have a backslash ('\') before it: AP seqret CL "tembl:ab*" aball.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI aball.seq FP /^>AB000095/ FP 4 /^>/ // ID seqret-ex11 UC seqret does not read in features by default because this results in UC slightly faster performance. If however you wish to read in features UC with your sequence and write them out on output, using '-feature' will UC change the default behaviour to use any features present in the sequence. UC N.B. use embl format for the output file as the default format 'fasta' UC reports the features in gff (file ".gff") AP seqret CL -feature IN tembl:x65923 IN embl::x65923.embl FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.embl FP /X65923/ // #################################################### # end of seqret examples for documentation #################################################### ID seqretall-ex AP seqret CL -auto @../../data/eclac.list test.out -osf fasta FI test.out FZ = 15619 FP 1 /^>J01636/ FP 3 /^>V0029/ FP 5 /^>/ // ID seqretall-ex2 AP seqret CL -auto tembl:v00296 test.out -osf fasta FI test.out FP 1 /^>V00296/ // ############################################################################# # should make output filename optional as it is rarely used ID seqretsplit-ex AP seqretsplit CL tembl:m1190* IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI m11903.fasta FZ = 861 FP /^>M11903 / FI m11904.fasta FZ = 710 FP /^>M11904 / FI m11905.fasta FZ = 654 FP /^>M11905 / // ##################################################### # Testing NCBI formatted ID lines are correctly split ##################################################### ID seqret-ncbi-gb AP seqret CL ../../data/testids.ncbi:GENBANK test.out -auto FI test.out FP 1 /^>/ FP /^>GENBANK G12345 / FP /^GENBANK$/ FZ = 58 // ID seqret-ncbi-embl AP seqret CL ../../data/testids.ncbi:EMBL test.out -auto FI test.out FP 1 /^>/ FP /^>EMBL E12345 / FP /^EMBL$/ FZ = 49 // ID seqret-ncbi-ddbj AP seqret CL ../../data/testids.ncbi:DDBJ test.out -auto FI test.out FP 1 /^>/ FP /^>DDBJ D12345 / FP /^DDB-$/ FZ = 49 // ID seqret-ncbi-pir AP seqret CL ../../data/testids.ncbi:PIR test.out -auto FI test.out FP 1 /^>/ FP /^>PIR PIR/ FP /^PIR$/ FZ = 40 // ID seqret-ncbi-prf AP seqret CL ../../data/testids.ncbi:PRF test.out -auto FI test.out FP 1 /^>/ FP /^>PRF Protein / FP /^PRF$/ FZ = 58 // ID seqret-ncbi-swissprt AP seqret CL ../../data/testids.ncbi:SWISS_PRT test.out -auto FI test.out FP 1 /^>/ FP /^>SWISS_PRT P01234/ FP /^SWISSPR-T$/ FZ = 64 // ID seqret-ncbi-pdb AP seqret CL ../../data/testids.ncbi:2PDBA test.out -auto FI test.out FP 1 /^>/ FP /^>2PDBA PDB / FP /^-PDB-A$/ FZ = 35 // ID seqret-ncbi-pat AP seqret CL ../../data/testids.ncbi:12345 test.out -auto FI test.out FP 1 /^>/ FP /^>12345 Patent/ FP /^PAT-K$/ FZ = 39 // ID seqret-ncbi-bbs AP seqret CL ../../data/testids.ncbi:GENINFO test.out -auto FI test.out FP 1 /^>/ FP /^>geninfo Geninfo/ FP /^GENINF-$/ FZ = 37 // ID seqret-ncbi-gnl AP seqret CL ../../data/testids.ncbi:E1234 test.out -auto FI test.out FP 1 /^>/ FP /^>e1234 General/ FP /^GNLPID$/ FZ = 68 // ID seqret-ncbi-ref1 AP seqret CL ../../data/testids.ncbi:REF_12345 test.out -auto FI test.out FP 1 /^>/ FP /^>REF_12345 NP_007225\.1 / FP /^REFSEQ$/ FZ = 54 // ID seqret-ncbi-ref2 AP seqret CL ../../data/testids.ncbi:NM_012488.1 test.out -auto FI test.out FP 1 /^>/ FP /^>NM_012488\.1 NM_012488\.1 / FP /^REFSEQ$/ FZ = 70 // ID seqret-ncbi-lcl AP seqret CL ../../data/testids.ncbi:LOCALID test.out -auto FI test.out FP 1 /^>/ FP /^>localid Local / FP /^L-CALID$/ FZ = 53 // ID seqret-ncbi-gi AP seqret CL ../../data/testids.ncbi:123456 test.out -auto FI test.out FP 1 /^>/ FP /^>123456 gi prefix/ FP /^GIPREFIX$/ FZ = 27 // ID seqret-ncbi-gigb AP seqret CL ../../data/testids.ncbi:GIGENBANK test.out -auto FI test.out FP 1 /^>/ FP /^>GIGENBANK G67890 / FP /^GIGENBANK$/ FZ = 52 // ID seqret-ncbi-gisp AP seqret CL ../../data/testids.ncbi:GISWISS_PRT test.out -auto FI test.out FP 1 /^>/ FP /^>GISWISS_PRT P01234 / FP /^GISWISSPR-T$/ FZ = 58 // ID seqret-ncbi-gnlblast AP seqret CL ../../data/testids.ncbi:BLAST test.out -auto FI test.out FP 1 /^>/ FP /^>Blast formatdb / FP /^BLAST$/ FZ = 46 // ##################################################### # Testing NCBI formatted ID lines are correctly reproduced ##################################################### ID seqret-ncbiout-gb AP seqret CL ../../data/testids.ncbi:GENBANK test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gb\|G12345\|GENBANK genbank / FP /^GENBANK$/ FZ = 61 // ID seqret-ncbiout-embl AP seqret CL ../../data/testids.ncbi:EMBL test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>emb\|E12345\|EMBL embl / FP /^EMBL$/ FZ = 53 // ID seqret-ncbiout-ddbj AP seqret CL ../../data/testids.ncbi:DDBJ test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>dbj\|D12345\|DDBJ DDBJ / FP /^DDB-$/ FZ = 53 // ID seqret-ncbiout-pir AP seqret CL ../../data/testids.ncbi:PIR test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>pir\|\|PIR / FP /^PIR$/ FZ = 45 // ID seqret-ncbiout-prf AP seqret CL ../../data/testids.ncbi:PRF test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>prf\|\|PRF / FP /^PRF$/ FZ = 63 // ID seqret-ncbiout-swissprt AP seqret CL ../../data/testids.ncbi:SWISS_PRT test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>sp\|P01234\|SWISS_PRT swissprot / FP /^SWISSPR-T$/ FZ = 67 // ID seqret-ncbiout-pdb AP seqret CL ../../data/testids.ncbi:2PDBA test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gnl\|pdb\|2PDBA PDB / FP /^-PDB-A$/ FZ = 43 // ID seqret-ncbiout-pat AP seqret CL ../../data/testids.ncbi:12345 test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gnl\|unk\|12345 Patent / FP /^PAT-K$/ FZ = 47 // ID seqret-ncbiout-bbs AP seqret CL ../../data/testids.ncbi:GENINFO test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gnl|unk|geninfo Geninfo / FP /^GENINF-$/ FZ = 45 // ID seqret-ncbiout-gnl AP seqret CL ../../data/testids.ncbi:E1234 test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gnl\|PID\|e1234 General/ FP /^GNLPID$/ FZ = 76 // ID seqret-ncbiout-ref1 AP seqret CL ../../data/testids.ncbi:REF_12345 test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>ref\|NP_007225\.1\|REF_12345 NCBI / FP /^REFSEQ$/ FZ = 58 // ID seqret-ncbiout-ref2 AP seqret CL ../../data/testids.ncbi:NM_012488.1 test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>ref\|NM_012488\.1\| NCBI / FP /^REFSEQ$/ FZ = 63 // ID seqret-ncbiout-lcl AP seqret CL ../../data/testids.ncbi:LOCALID test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>lcl\|localid Local / FP /^L-CALID$/ FZ = 57 // ID seqret-ncbiout-gi AP seqret CL ../../data/testids.ncbi:123456 test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gi\|123456 gi prefix/ FP /^GIPREFIX$/ FZ = 30 // ID seqret-ncbiout-gigb AP seqret CL ../../data/testids.ncbi:GIGENBANK test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gi\|123456\|gb\|G67890\|GIGENBANK gi / FP /^GIGENBANK$/ FZ = 65 // ID seqret-ncbiout-gisp AP seqret CL ../../data/testids.ncbi:GISWISS_PRT test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gi\|234567\|sp\|P01234\|GISWISS_PRT gi / FP /^GISWISSPR-T$/ FZ = 71 // ID seqret-ncbiout-gnlblast AP seqret CL ../../data/testids.ncbi:BLAST test.out -osf ncbi -auto FI test.out FP 1 /^>/ FP /^>gnl\|BL_ORD_ID\|0 Blast formatdb / FP /^BLAST$/ FZ = 62 // ############################################### # seqret (sequence input) associated qualifiers ############################################### ID seq-end-fasta AQ seqretsingle CL tembl:v00294 -send 100 -out test.out -auto FI test.out FZ = 168 FP 1 /^>/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-begin-fasta AQ seqretsingle CL tembl:v00294 -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 117 FP 1 /^>/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-rev-fasta AQ seqretsingle CL tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 117 FP 1 /^>/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seq-end-msf AQ seqretsingle CL tembl:v00294 -send 100 -out test.out -osf msf -auto FI test.out FZ = 395 FP 1 /^ +Name: / FP / +Name: V00294 .* Check: 8066/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-begin-msf AQ seqretsingle CL tembl:v00294 -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: V00294 .* Check: 2937/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seq-rev-msf AQ seqretsingle CL tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: V00294 .* Check: 9768/ FP /^V00294 ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqall-end-fasta AP seqret CL "tembl:v0029*" -send 100 -out test.out -auto FI test.out FZ = 517 FP 3 /^>/ FP /^ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqall-begin-fasta AP seqret CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 364 FP 3 /^>/ FP /^ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/ FP /^aaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcg\n/ // ID seqall-rev-fasta AP seqret CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 364 FP 3 /^>/ FP /^atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqall-end-msf AP seqret CL "tembl:v0029*" -send 100 -out test.out -osf msf -auto FI test.out FZ = 751 FP 3 / +Name: / FP / +Name: V00294 .* Check: 8066/ FP / +Name: V00295 .* Check: 6545/ FP /^V00296 accatgattacggattcactggccgtcgttttacaacgtcgtgactggga\n/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqall-begin-msf AP seqret CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 498 FP 3 / +Name: / FP / +Name: V00294 .* Check: 2937/ FP / +Name: V00295 .* Check: 1564/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FP /^V00295 ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/ // ID seqall-rev-msf AP seqret CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 498 FP 3 / +Name: / FP / +Name: V00294 .* Check: 9768/ FP / +Name: V00295 .* Check: 3152/ FP /^V00294 ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FP /^V00295 atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/ // ID seqset-end-fasta AQ seqretset CL "tembl:v0029*" -send 100 -out test.out -auto FI test.out FZ = 517 FP 3 /^>/ FP /^ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqset-begin-fasta AQ seqretset CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 364 FP 3 /^>/ FP /^ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/ FP /^aaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcg\n/ // ID seqset-rev-fasta AQ seqretset CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 364 FP 3 /^>/ FP /^atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ // ID seqset-end-msf AQ seqretset CL "tembl:v0029*" -send 100 -out test.out -osf msf -auto FI test.out FZ = 751 FP 3 / +Name: / FP / +Name: V00294 .* Check: 8066/ FP / +Name: V00295 .* Check: 6545/ FP /^V00296 accatgattacggattcactggccgtcgttttacaacgtcgtgactggga\n/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ // ID seqset-begin-msf AQ seqretset CL "tembl:v0029*" -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 498 FP 3 / +Name: / FP / +Name: V00294 .* Check: 2937/ FP / +Name: V00295 .* Check: 1564/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FP /^V00295 ataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaat\n/ // ID seqset-rev-msf AQ seqretset CL "tembl:v0029*" -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 498 FP 3 / +Name: / FP / +Name: V00294 .* Check: 9768/ FP / +Name: V00295 .* Check: 3152/ FP /^V00294 ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FP /^V00295 atttccttacgcgaaatacgggcagacatggcctgcccggttattattat\n/ // ###################################################### # end of seqret (sequence input) associated qualifiers ###################################################### ########################################################### # seqret (sequence and feature input) associated qualifiers ########################################################### ID featseq-end-fasta AQ seqretsingle CL -feat tembl:v00294 -send 100 -out test.out -auto FI test.out FZ = 168 FP 1 /^>/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FC = 7 FZ = 1290 FP /^#!Type DNA\n/ FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true/ // ID featseq-begin-fasta AQ seqretsingle CL -feat tembl:v00294 -sbegin 51 -send 100 -out test.out -auto FI test.out FP 1 /^>/ FZ = 117 FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 1323 FP /^#!Type DNA\n/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseq-rev-fasta AQ seqretsingle CL -feat tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 117 FP 1 /^>/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 1323 FP /^#!Type DNA\n/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseq-end-embl AQ seqretsingle CL -feat tembl:v00294 -send 100 -out test.out -osf embl -auto FI test.out FZ = 2947 FP 1 /^ID / FP 1 /^FH / FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/ FP /^FT CDS 31\.\.>100\n/ // ID featseq-begin-embl AQ seqretsingle CL -feat tembl:v00294 -sbegin 51 -send 100 -out test.out -osf embl -auto FI test.out FZ = 2862 FP 1 /^ID / FP 1 /^FH / FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/ FP /^FT CDS <1\.\.>50\n/ // ID featseq-rev-embl AQ seqretsingle CL -feat tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -osf embl -auto FI test.out FZ = 2886 FP 1 /^ID / FP 1 /^FH / FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/ FP /^FT CDS complement[(]<1\.\.>50[)]\n/ // ID featseq-end-msf AQ seqretsingle CL -feat tembl:v00294 -send 100 -out test.out -osf msf -auto FI test.out FZ = 395 FP 1 /^ +Name: / FP / +Name: V00294 .* Check: 8066/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FC = 7 FZ = 1290 FP /^#!Type DNA\n/ FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/ // ID featseq-begin-msf AQ seqretsingle CL -feat tembl:v00294 -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: V00294 .* Check: 2937/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 1323 FP /^#!Type DNA\n/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseq-rev-msf AQ seqretsingle CL -feat tembl:v00294 -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 268 FP 1 / +Name: / FP / +Name: V00294 .* Check: 9768/ FP /^V00294 ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 1323 FP /^#!Type DNA\n/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqall-end-fasta AP seqret CL -feat @../../data/eclac.list -send 100 -out test.out -auto FI test.out FZ = 877 FP 5 /^>/ FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7580 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/ // ID featseqall-begin-fasta AP seqret CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 622 FP 5 /^>/ FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7418 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqall-rev-fasta AP seqret CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 622 FP 5 /^>/ FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 7424 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqall-end-embl AP seqret CL -feat @../../data/eclac.list -send 100 -out test.out -osf embl -auto FI test.out FZ = 29920 FP 5 /^ID / FP 5 /^FH / FP /^ +caattcaggg tggtgaatgt gaaaccagta acgttatacg +100\n/ FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/ FP /^FT CDS 31\.\.>100\n/ // ID featseqall-begin-embl AP seqret CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf embl -auto FI test.out FZ = 29150 FP 5 /^ID / FP 5 /^FH / FP /^ +ggaagagagt caattcaggg tggtgaatgt gaaaccagta acgttatacg +50/ FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/ FP /^FT CDS 29\.\.>50\n/ FP /^FT CDS <1\.\.>50\n/ // ID featseqall-rev-embl AP seqret CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf embl -auto FI test.out FZ = 29294 FP 5 /^ID / FP 5 /^FH / FP /^ +cgtataacgt tactggtttc acattcacca ccctgaattg actctcttcc +50\n/ FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/ FP /^FT CDS complement[(]<1\.\.22[)]\n/ FP /^FT CDS complement[(]<1\.\.>50[)]\n/ // ID featseqall-end-msf AP seqret CL -feat @../../data/eclac.list -send 100 -out test.out -osf msf -auto FI test.out FZ = 1107 FP 5 / +Name: / FP / +Name: J01636 .* Check: 4203/ FP / +Name: V00294 .* Check: 8066/ FP /^J01636 ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7580 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/ // ID featseqall-begin-msf AP seqret CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: J01636 .* Check: 1328/ FP / +Name: V00294 .* Check: 2937/ FP /^J01636 ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7418 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqall-rev-msf AP seqret CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: J01636 .* Check: 2885/ FP / +Name: V00294 .* Check: 9768/ FP /^J01636 cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^V00294 ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 7424 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqset-end-fasta AQ seqretset CL -feat @../../data/eclac.list -send 100 -out test.out -auto FI test.out FZ = 877 FP 5 /^>/ FP /^caattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^gagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7580 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/ // ID featseqset-begin-fasta AQ seqretset CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -auto FI test.out FZ = 622 FP 5 /^>/ FP /^ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7418 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqset-rev-fasta AQ seqretset CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -auto FI test.out FZ = 622 FP 5 /^>/ FP /^cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 7424 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqset-end-embl AQ seqretset CL -feat @../../data/eclac.list -send 100 -out test.out -osf embl -auto FI test.out FZ = 29920 FP 5 /^ID / FP 5 /^FH / FP /^ +caattcaggg tggtgaatgt gaaaccagta acgttatacg +100\n/ FP /^ +gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +100\n/ FP /^FT CDS 31\.\.>100\n/ // ID featseqset-begin-embl AQ seqretset CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf embl -auto FI test.out FZ = 29150 FP 5 /^ID / FP 5 /^FH / FP /^ +ggaagagagt caattcaggg tggtgaatgt gaaaccagta acgttatacg +50/ FP /^ +cgatgtcgca gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg +50/ FP /^FT CDS 29\.\.>50\n/ FP /^FT CDS <1\.\.>50\n/ // ID featseqset-rev-embl AQ seqretset CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf embl -auto FI test.out FZ = 29294 FP 5 /^ID / FP 5 /^FH / FP /^ +cgtataacgt tactggtttc acattcacca ccctgaattg actctcttcc +50\n/ FP /^ +ccacgcggga aacggtctga taagagacac cggcatactc tgcgacatcg +50\n/ FP /^FT CDS complement[(]<1\.\.22[)]\n/ FP /^FT CDS complement[(]<1\.\.>50[)]\n/ // ID featseqset-end-msf AQ seqretset CL -feat @../../data/eclac.list -send 100 -out test.out -osf msf -auto FI test.out FZ = 1107 FP 5 / +Name: / FP / +Name: J01636 .* Check: 4203/ FP / +Name: V00294 .* Check: 8066/ FP /^J01636 ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7580 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t79\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t31\t100\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;/ // ID featseqset-begin-msf AQ seqretset CL -feat @../../data/eclac.list -sbegin 51 -send 100 -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: J01636 .* Check: 1328/ FP / +Name: V00294 .* Check: 2937/ FP /^J01636 ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg\n/ FP /^V00294 cgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtgg\n/ FI test.gff FZ = 7418 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t29\t50\t\.\t[+]\t0\tID=\S+;featflags=end_after:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[+]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ID featseqset-rev-msf AQ seqretset CL -feat @../../data/eclac.list -sbegin 51 -send 100 -srev -out test.out -osf msf -auto FI test.out FZ = 728 FP 5 / +Name: / FP / +Name: J01636 .* Check: 2885/ FP / +Name: V00294 .* Check: 9768/ FP /^J01636 cgtataacgttactggtttcacattcaccaccctgaattgactctcttcc\n/ FP /^V00294 ccacgcgggaaacggtctgataagagacaccggcatactctgcgacatcg\n/ FI test.gff FZ = 7424 FP 5 /^#!Type DNA/ FP /^J01636\tEMBL\tCDS\t1\t22\t\.\t[-]\t0\tID=\S+;featflags=start_before:true;.*gene=lacI;/ FP /^V00294\tEMBL\tCDS\t1\t50\t\.\t[-]\t0\tID=\S+;featflags=start_before:true,end_after:true;/ // ################################################################## # end of seqret (sequence and feature input) associated qualifiers ################################################################## ID seqretsetall-ex AP seqretsetall CL -osf phylip IN ../../data/globins-all.phy IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins-all.phylip FZ = 3135 FP 1 /^ 7 164\n/ FP 1 /^ 7 167\n/ FP /^ FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE\n/ FP /^ FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF\n/ // ID seqxref-ex AP seqxref CL tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.seqxref FC = 20 FP /^#tembl-id:X13776: 20\n/ FP 19 /[^:\s]+:[^:\s]+\n/ FP 3 /^UniProtKB/Swiss-Prot:/ FP 3 /^PDB:/ FP /^taxon:287\n/ // ID seqxrefget-ex AP seqxrefget CL tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.seqxrefget FC = 20 FP /^#tembl-id:X13776: 20\n/ FP 19 /[^:\s]+:[^:\s]+\n/ FP 3 /^entret UniProtKB/Swiss-Prot:/ FP 3 /^textget PDB:/ FP /^taxtext taxon:287\n/ // ID servertell-ex AP servertell CL srs FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP /^SERVER srs \[\n/ FP /^# databases: 21\n/ FP 1 /^ url: "\S+"\n/ // ID showalign-ex AP showalign IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FZ = 2003 FP /^HBB_HUMAN --------VH\.tPE\.K\.A\.TaL\.G\.V\.-VD\.\.\.\.E\.\.GR-\.LVvY\.WT\.R\.\.Es\.GD\.\.T\n/ FP /^Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx\n/ // ID showalign-ex2 UC Show non-identities between the sequences AP showalign CL -show=n IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex3 UC Show all of the sequences AP showalign CL -show=a IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex4 UC Show identities between the sequences AP showalign CL -show=i IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex5 UC Show similarities between the sequences AP showalign CL -show=s IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex6 UC Show dissimilarities between the sequences AP showalign CL -show=d IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex7 UC Use the first sequence as the reference to compare to: AP showalign CL -ref=1 IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex8 UC Show a range of sequences in uppercase, everything else in lowercase AP showalign CL -nocon -ref=1 -sl -upper 9-15 -nosimilarcase IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex9 UC Display the sequences in alphabetic order: AP showalign CL -order=a IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex10 UC Display the sequences in order of similarity to the reference sequence AP showalign CL -order=s IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex11 UC Format for HTML and highlight some interesting regions in different colours: AP showalign CL -html -high "4-13 green 43-43 red 51-56 blue" IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showalign-ex12 UC No consensus line at the bottom UC No ruler line UC No numbers line UC Don't repeat the reference sequence at the bottom of the sequences UC Use sequence 1 as the reference sequence UC Display residues from position 10 to 30 only AP showalign CL -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30 IN ../../data/globins.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.showalign FP /HBB_HUMAN/ // ID showdb-ex UC Display information on the currently available databases: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+Protein\s+OK\s+OK\s+OK/ FP /^tembl\s+Nucleotide\s+OK\s+OK\s+OK/ // ID showdb-ex2 UC Write the results to a file: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -outfile showdb.out FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI showdb.out FP /^tsw\s+Protein\s+OK\s+OK\s+OK/ FP /^tembl\s+Nucleotide\s+OK\s+OK\s+OK/ // ID showdb-ex3 UC Display information on one explicit database: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -database tsw FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+Protein\s+OK\s+OK\s+OK/ FP 0 /^tembl/ // ID showdb-ex4 UC Display information on the databases formatted in HTML: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tswProteinOK/ FP /^temblNucleotideOK/ // ID showdb-ex5 UC Display protein databases only: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -nonucleic FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+Protein\s+OK\s+OK\s+OK/ FP 0 /^[^#]\S*\s+Nucleotide/ // ID showdb-ex6 UC Display the information with no headings: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -noheading FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /\A\S+\s+[PN][a-z]+\s+/ FP 0 /\A#/ // ID showdb-ex7 UC Display just a list of the available database names: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -noheading -notype -noid -noquery -noall -nocomment -auto FI stdout FP /^tsw\s+\n/ FP /^tembl\s+\n/ // ID showdb-ex8 UC Display only the names and types: AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -only -type FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+Protein\s+\n/ FP /^tembl\s+Nucleotide\s+\n/ // ID showdb-ex9 UC Display everything AP showdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME CL -full FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^tsw\s+Protein\s+OK\s+OK\s+OK\s+emblcd\s+id,acc,sv,des,org,key\s+special\s+\S+\s+Swissprot native format with EMBL CD-ROM index\n/ // ID showfeat-ex AP showfeat IN tembl:x65921 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.showfeat FZ = 1429 FP /\|=+\| 2016\n/ FP 5 / mRNA\n/ FP /-> source\n/ // ID showfeat-ex2 UC Display 'joined' features on one line with positions: AP showfeat CL -joinfeat -pos IN tembl:x65921 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.showfeat FZ = 1150 FP /\|=+\| 2016\n/ FP /mRNA\n/ FP /source\n/ // ID showfeat-ex3 UC Display just positions and names of CDS features - this can be used as a regions file in showseq: AP showfeat CL -typematch CDS -width 0 -noid -nodesc -noscale -pos IN tembl:x65921 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.showfeat FZ = 54 FP /CDS/ // ID showorf-ex AP showorf IN tembl:x13776 IN IN FI stderr FC = 10 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showorf FZ = 22690 FP /^F1 +1 G T A G R A S A R S P P A G R R E 17\n/ FP /^R2 +106 Y R Q G L M Q E I V V L R A V P 91\n/ // ID showpep-ex AP showpep CL tsw:laci_ecoli -sbeg 1 -send 100 IN IN FI stderr FC = 7 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 1581 FP 1 /^\s+\|=+\|\n\s+polypeptide_domain note="/ FP 1 /^\s+\|=+\|\s+\|=+\|\n\s+DNA_contact note="/ FP 2 /^\s+\|\n\s+mutated_variant_site note="/ // ID showpep-ex2 UC The standard list of output formats are only a small selection of the UC possible ways in which a sequence might be displayed. Precise control UC over the output format is acheived by selecting the qualifier '-format 0' UC (Option 0 in the list of things to display). For example, UC by choosing format '0' and then specifying that we want to display the UC things: 'b,t,s', we will output the sequence in the following way: AP showpep CL tsw:laci_ecoli -sbeg 1 -send 120 IN 0 IN b,t,s IN FI stderr FC = 14 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 323 FP 2 /^ ----:----\|----:----\|----:----\|----:----\|----:----\|----:----\|\n/ FP /^ SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS/ // ID showpep-ex3 UC Display only the sequence: AP showpep CL tsw:laci_ecoli -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 123 FP /^ MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ\n/ FP /^ SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE\n/ // ID showpep-ex4 UC Protein sequence can be displayed in three-letter codes. UC (The codes are displayed downwards, so the first code is 'Met'): AP showpep CL tsw:rs24_takru -three -format 2 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rs24_takru.showpep FZ = 1296 FP /^ MAATVT/ // ID showpep-ex5 UC Number the sequence lines in the margin: AP showpep CL tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 166 FP /^ 61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 100\n/ // ID showpep-ex6 UC Start the numbering at a specified value ('123' in this case): AP showpep CL tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number -offset 123 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 167 FP /^ 183 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 222\n/ // ID showpep-ex7 UC Make selected regions uppercase. (Use '-slower' to force the rest of UC the sequence to be lowercase). AP showpep CL tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -slower -upper CL "17-17,22-22" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 159 FP / mkpvtlydvaeyagvsYqtvsRvvnqashvsaktrekveaamaelnyipnrvaqqlagkq\n/ FP / slligvatsslalhapsqivaaiksradqlgasvvvsmve\n/ // ID showpep-ex9 UC Add your own annotation to the display: AP showpep CL tsw:laci_ecoli -sbeg 1 -send 100 -format 2 -send 120 CL -annotation "6-25 binding site 17-17 SNP 22-22 SNP" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI laci_ecoli.showpep FZ = 2001 FP /binding site/ FP /^ SNP SNP\n/ // ID showseq-ex AP showseq CL tembl:x13776 -sbeg 1 -send 100 IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 729 FP 2 /^\s+\|=+\|\n\s+promoter note="/ // ID showseq-ex2 UC The standard list of output formats are only a small selection of the UC possible ways in which a sequence might be displayed. Precise control UC over the output format is acheived by selecting the qualifier '-format 0' UC (Option 0 in the list of things to display). For example, UC by choosing format '0' and then specifying that we want to display the UC things: 'b,s,t,c', we will output the sequence in the following way: AP showseq CL tembl:x13776 -sbeg 1 -send 120 IN 0 IN b,s,t,c IN FI stderr FC = 28 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 511 FP /^ ggtacc/ // ID showseq-ex3 UC Display only the sequence: AP showseq CL tembl:x13776 -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 123 FP /^ ggtacc/ FP /^ ctacctggcgagcctggagcacgagcgggttcgcttcgta\n/ // ID showseq-ex4 UC Number the sequence lines in the margin: AP showseq CL tembl:x13776 -sbeg 1 -send 100 -format 1 -number IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 212 FP /^ 1 ggtacc/ // ID showseq-ex5 UC Start the numbering at a specified value ('123' in this case): AP showseq CL tembl:x13776 -sbeg 1 -send 100 -format 1 -number -offset 123 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 213 FP /^ 123 ggtacc/ // ID showseq-ex6 UC Make selected regions uppercase. UC (Use '-slower' to force the rest of the sequence to be lowercase). AP showseq CL tembl:x13776 -sbeg 1 -send 100 -format 1 -slower CL -upper "8-24,65-81" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 205 FP /^ ggtaccgCTGGCCGAGCATCTGCTcgatcaccaccagccgggcgacgggaactgcacgat\n/ FP /^ ctacCTGGCGAGCCTGGAGCAcgagcgggttcgcttcgta\n/ // ID showseq-ex7 UC Translate selected regions: AP showseq CL tembl:x13776 -sbeg 1 -send 120 -format 5 -trans 25-49,66-76 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 1221 FP /R S P P A G R R V/ FP /A S L/ // ID showseq-ex8 UC Add your own annotation to the display: AP showseq CL tembl:x13776 -sbeg 1 -send 100 -format 2 -send 120 -annotation "13-26 binding site 15-15 SNP" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.showseq FZ = 919 FP /binding site/ // ID showserver-ex UC Display information on the currently available servers: AP showserver PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 20 FP /^srs\s+text\s+Unknown\s+OK\s+OK\s+OK\s+21\s+\S+server\.srs/ // ID shuffleseq-ex UC This makes two randomised copies of the input sequence: AP shuffleseq CL -shuffle 2 IN tembl:L48662 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI l48662.fasta FZ = 950 FP 2 /^>L48662/ FP /^agccgg\n/ FP /^cctcgc\n/ // # fix output file in example ID sigcleave-ex AP sigcleave IN tsw:ach2_drome IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ach2_drome.sig FP /^[(]1[)] Score 13\.739 length 13 at residues 29->41\n/ FP /^ Sequence: LLVLLLLCETVQA\n/ FP 9 /^ Sequence: / // ID sigcleave-multi AP sigcleave IN tsw:a* IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ach2_drome.sig FP /^[(]1[)] Score 13\.739 length 13 at residues 29->41\n/ FP /^ Sequence: LLVLLLLCETVQA\n/ FP 28 /^ Sequence: / FP 5 /^# No scores over 3\.50\n/ FP 17 /^# Reporting scores over 3\.50\n/ FP 17 /^# Sequence: / // ID silent-ex PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA AP silent IN tembl:x65923 IN ecori,hindiii IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.silent FC = 39 FP /^ +267 +272 +[-] +HindIII +AAGCTT +268 +A\.A +Yes +A->T\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 1\n/ // ID silent-seqs PP EMBOSS_DATA=../rebaseextract-keep/ PP export EMBOSS_DATA AP silent CL -sshow -tshow IN tembl:x65923 IN ecori,hindiii IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.silent FC = 75 FP /^ +267 +272 +[-] +HindIII +AAGCTT +268 +A\.A +Yes +A->T\n/ FP /^\n/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 1\n/ // ID sixpack-ex AP sixpack IN tembl:x13776 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.sixpack FZ = 25376 FP /^ P P A W A G D R S H E R Q L A A R Q P A F1\n/ FP /^ R Q H G R G T A P M S A N S L L G S L R F2\n/ FP /^ A S M G G G P L P [*] A P T R C S A A C A F3\n/ FP /^ 1261 ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg 1320\n/ FI x13776.fasta FZ = 9445 FP /^>X13776_2_ORF4 Translation of X13776 in frame 2, ORF 4, threshold 1, 210aa\n/ FP /^PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP\n/ FP 67 /^>/ // ID sixpack-mstart AP sixpack CL -mstart IN tembl:x13776 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.sixpack FZ = 25376 FP /^ P P A W A G D R S H E R Q L A A R Q P A F1\n/ FP /^ R Q H G R G T A P M S A N S L L G S L R F2\n/ FP /^ A S M G G G P L P [*] A P T R C S A A C A F3\n/ FP /^ 1261 ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg 1320\n/ FI x13776.fasta FZ = 4506 FP /^>X13776_2_ORF2 Translation of X13776 in frame 2, ORF 2, threshold 1, 196aa\n/ FP /^MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI\n/ FP 30 /^>/ // ID sirna-ex AP sirna IN tembl:x65923 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.sirna FC = 114 FP /GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 85\n/ FI x65923.fasta FC = 170 FP /aaaagtgagaggtcagactccta/ // ID sirna-ex2 UC Show the first two bases of the 23 base target region in brackets. UC These do not form part of the sequence to be ordered, but it is useful UC to see if the 23 base region starts with an 'AA'. AP sirna CL -context IN tembl:x65923 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.sirna FC = 118 FP /\(AA\)GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 85\n/ FI x65923.fasta FZ = 6120 FP /aaaagtgagaggtcagactccta/ // ID sizeseq-ex AP sizeseq CL -osformat swiss IN ../../data/globins.fasta IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.swiss FC = 49 FP /\AID HBA_HUMAN Reviewed; 141 AA.\n/ // ID skipredundant-ex AP skipredundant CL -threshold 80 -redundant "" IN ../../data/globins.fasta IN IN IN IN FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins.keep FC = 20 FP 5 /^>/ FI globins.redundant FC = 8 FP 2 /^>/ // ID skipseq-ex UC This does not skip any sequences. It is exactly equivalent to seqret: AP skipseq IN @../../data/eclac.list IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.fasta FZ = 15619 FP 5 /^>/ // ID skipseq-ex2 UC This skips the first input sequence, writing out the others: AP skipseq CL -skip 1 IN @../../data/eclac.list IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.fasta FZ = 7940 FP 4 /^>/ // ID splitsource-ex UC Split a sequence into original subsequences AP splitsource CL qasrswww:A01139 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI a01139.fasta FZ = 579 FP /\A>A01139_1_1-81/ FP /^>A01139_1_1-81 organism="Lactococcus lactis"/ FP /^>A01139_2_82-279 organism="Hirudo medicinalis"/ FP 2 /^>/ // ID splitter-ex UC Split a sequence into sub-sequences of 10,000 bases (the default size) with no overlap between the sub-sequences: AP splitter CL tembl:BA000025 ba000025.split FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ba000025.split FZ = 2287126 FP /\A>BA000025_1-10000/ FP /^>BA000025_10001-20000/ FP /^>BA000025_90001-100000/ FP 223 /^>/ // ID splitter-ex2 UC Split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence: AP splitter CL tembl:BA000025 ba000025.split -size=50000 -over=3000 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ba000025.split FZ = 2414678 FP /\A>BA000025_1-50000/ FP /^>BA000025_47001-97000/ FP 48 /^>/ // # update example ID stretcher-ex AP stretcher CL tsw:hba_human tsw:hbb_human IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.stretcher FZ > 1442 FP /^# Matrix: EBLOSUM62\n/ FP /^# Gap_penalty: 12\n/ FP /^# Extend_penalty: 2\n/ FP /^# Identity: +65/149 \(43\.6%\)\n/ FP /^# Score: 277\n/ FP /^HBA_HU MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-D\n/ FP /^HBB_HU MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD\n/ // ID stssearch-ex AP stssearch IN @../../data/eclac.list IN ../../data/lac.primers IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.stssearch FZ = 719 FP /^J01636: PrimA PrimerA matched at 532\n/ FP /^J01636: \(rev\) PrimA PrimerB matched at 689\n/ // ID supermatcher-ex TI 400 AP supermatcher CL @../../data/eclac.list tembl:j01636 -word 50 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI j01636.supermatcher FZ > 71230 FP /^J01636 +1 / FP /^# Score: 37385\.0/ FP 5 /^# Score: / FP /^X51872 +1801 [acgt]+ +1832\n/ // ID supermatcher-range TI 400 AP supermatcher CL @../../data/eclac.list tembl:j01636 -word 50 -sbegin2 101 -send2 -101 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI j01636.supermatcher FZ > 69555 FP /^J01636 +101 / FP /^# Score: 36385\.0/ FP 5 /^# Score: / FP /^X51872 +1701 [acgt]+ +1732\n/ // ID syco-ex AP syco CL -plot -cfile Epseae.cut IN tembl:x13776 IN ps FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 16 FP /^Created syco\.ps\n/ FI syco.ps FC = 971 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID taxget-ex AP taxget CL ttax:9606 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9606.tax FP /^id: 9606\n/ FP 1 /^id: / FP 3 /name: / FP 1 /^parent: 9605\n/ FP 1 /^scientific name: Homo sapiens\n/ FC = 17 // ID taxgetdown-ex AP taxgetdown CL ttax:9605 -oformat excel IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9605.excel FP /^741158\t9605\tspecies\tY\tHomo sp. Altai\n/ FP 2 /\tHomo / FC = 2 // ID taxgetrank-ex AP taxgetrank CL ttax:9606 -oformat excel IN IN FI stderr FC = 31 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9606.excel FP /9604\t314295\tfamily\tN\tHominidae\n/ FP 1 /order/ FP 0 /\tY\t/ FC = 6 // ID taxgetrank-ex2 AP taxgetrank CL ttax:9606 -oformat excel IN * IN FI stderr FC = 31 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9606.excel FP /9604\t314295\tfamily\tN\tHominidae\n/ FP 4 /order/ FP 0 /\tY\t/ FC = 14 // ID taxgetrank-ex3 AP taxgetrank CL ttax:9606 -oformat excel -hidden IN * IN FI stderr FC = 31 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9606.excel FP /9604\t314295\tfamily\tN\tHominidae\n/ FP 5 /order/ FP /^314293\t376913\tinfraorder\tY\tSimiiformes\n/ FP 15 /\tY\t/ FC = 29 // ID taxgetspecies-ex AP taxgetspecies CL taxon-tax:hominidae -oformat excel IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9604.excel FP /^741158\t9605\tspecies\tY\tHomo sp. Altai\n/ FP 2 /\tHomo / FP 4 /\tPongo / FP 2 /\tGorilla / FP 4 /\tPan / FC = 12 // ID taxgetup-ex AP taxgetup CL ttax:9606 -oformat excel IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9606.excel FP 1 /^9605\t207598\tgenus\tN\tHomo\n/ FP 0 /^207598\t/ FC = 14 // ID taxgetup-ex2 AP taxgetup CL ttax:9606 -hidden -oformat excel IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 9606.excel FP 1 /^9605\t207598\tgenus\tN\tHomo\n/ FP 1 /^207598\t/ FC = 29 // ID tcode-ex AP tcode IN tembl:x65921 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.tcode FC = 635 FP /^ 1 200 [+] 0\.692 Non-coding/ FP /^ 22 221 [+] 0\.901 No opinion/ FP /^ 37 236 [+] 1\.043 Coding/ // ID tcode-ex2 UC Produce a graphical plot CL -plot -graph cps AP tcode IN tembl:x65921 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 17 FP /^Created tcode\.ps\n/ FI tcode.ps FC = 390 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID tcode-twoseqs UC Produce a graphical plot CL -plot -graph cps AP tcode IN tembl:{x65921,x13776} IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 17 FP /^Created tcode\.ps\n/ FI tcode.ps FC = 708 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 2\n/ // ID textget-ex AP textget CL "srs:unilib:99" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.text FC = 37 FP /^> 99\n/ // ID textsearch-ex UC Search for 'lactose': AP textsearch CL "tsw:*" "lactose" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 12s1_arath.textsearch FZ = 167 FP /^tsw-id:LACI_ECOLI LACI_ECOLI P03023\s+Lactose operon repressor/ FP /^tsw-id:LACY_ECOLI LACY_ECOLI P02920\s+Lactose permease/ // ID textsearch-ex2 UC Search for 'lactose' or 'permease' in E.coli proteins: AP textsearch CL "tsw:*_ecoli" "lactose | permease" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI bgal_ecoli.textsearch FZ = 178 FP /^tsw-id:LACI_ECOLI LACI_ECOLI P03023\s+Lactose operon repressor/ FP /^tsw-id:LACY_ECOLI LACY_ECOLI P02920\s+Lactose permease/ // # update example ID textsearch-ex3 UC Output a search for 'lacz' formatted with HTML to a file: AP textsearch CL "tembl:*" "lacz" -html -outfile embl.lacz.html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI embl.lacz.html FZ = 351 FP /^tembl-id:J01636J01636J01636\s+E\.coli lactose operon with lacI, lacZ, lacY and lacA genes\./ // ID tfextract-keep ## Note: yeast is now fungi rather than plant. DL keep AP tfextract PP EMBOSS_DATA=./ PP export EMBOSS_DATA IN ../../data/site.dat FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI tffungi FZ = 121 FP /^Y\$ADH1_02/ FI tfinsect FZ = 0 FI tfvertebrate FZ = 676 FC = 7 FP /^HS\$ALBU_01 +tGGTTAGtaattactaa R00077 T01951; HNF-1C;Quality: 1; Species: human, Homo sapiens\./ FP 5 /^HS\$ALBU/ FP 2 /^MOUSE/ FI tfplant FZ = 0 FI tfother FZ = 0 // ID tfm-ex AP tfm CC wossname documentation subject to updates - will break file size test CC On some systems 'more' also reports the filename at the start of the output CL wossname FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ > 43000 FP 1 /^ +Finds programs by keywords in their short description\n/ FP 1 /^ +-explode/ // ID tfscan-ex CC Needs tfextract to reformat TRANSFAC data AP tfscan PP EMBOSS_DATA=../tfextract-keep/ PP export EMBOSS_DATA IN tembl:k00650 IN v IN IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI k00650.tfscan FZ = 1614 FC = 34 FP /^ 3287 3292 \+ R04413 T00702; .* Mus musculus\. ttcctc\n/ // ID tmap-ex AP tmap CL ../../data/opsd.msf -out tmap.res -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 16 FP /^Created tmap\.ps\n/ FI tmap.res FZ = 2337 FP 3 /^ 43 70 1 YMF.*KLRT\n/ FP /^# Reported_sequences: 3\n/ FP /^# Reported_hitcount: 21\n/ FI tmap.ps FC = 1409 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID tmap-single AP tmap CL tsw:opsd_human -out tmap.res -graph cps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 16 FP /^Created tmap\.ps\n/ FI tmap.res FZ = 1696 FP 2 /^ 43 69 1 YMFLLIVLGFPINFLTLYVTVQHKKLR\n/ FP /^# Reported_sequences: 2\n/ FP /^# Reported_hitcount: 14\n/ FI tmap.ps FC = 1426 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID tranalign-ex AP tranalign CL ../../data/tranalign.seq ../../data/tranalign.pep tranalign2.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI tranalign2.seq FZ = 2375 FP /^>HSFAU1/ FP /^cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg/ // # update the examples ID transeq-ex UC To translate a sequence in the first frame (starting at the first base and proceeding to the end): AP transeq CL tembl:x13776 amir.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 821 FP /^>X13776_1/ FP /^GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR\*SACCSP\n/ // ID transeq-ex2 UC To translate a sequence in the second frame: AP transeq CL tembl:x13776 amir.pep -frame=2 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 820 FP /^>X13776_2/ FP /^VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR\*ATVTGEETDGIAPGAAADRPAVLR\n/ // ID transeq-ex3 UC To translate a sequence in the first frame in the reverse sense (starting at the last frame 1 codon and proceeding to the start): AP transeq CL tembl:x13776 amir.pep -frame=-1 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 820 FP /^>X13776_4/ FP /^SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS\*AIFRIGSRRFIAS\n/ // ID transeq-ex4 UC To translate a sequence in all three forward frames: AP transeq CL tembl:x13776 amir.pep -frame=F FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 2461 FP /^>X13776_1/ FP /^>X13776_2/ FP /^>X13776_3/ FP /^CWARSAVGRWR\*STSWSAC\*APASRST\*SFPQQPGRAR\*RPER\*PCYSLLPICGWPPTSS\n/ // ID transeq-ex5 UC To translate a sequence in all three reverse frames: AP transeq CL tembl:x13776 amir.pep -frame=R FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 2461 FP /^>X13776_4/ FP /^>X13776_5/ FP /^SNQTALRNSTAPTYSRTSPSMMTIPLLLLFWSARIAQADGSFPSNS\*AIFRIGSRRFIAS\n/ FP /^LEELVGGHPQIGKSE\*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA\n/ FP /^>X13776_6/ // ID transeq-ex6 UC To translate a sequence in all six forward and reverse frames: AP transeq CL tembl:x13776 amir.pep -frame=6 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 4922 FP /^>X13776_1/ FP /^>X13776_2/ FP /^>X13776_3/ FP /^>X13776_4/ FP /^>X13776_5/ FP /^>X13776_6/ FP /^LEELVGGHPQIGKSE\*QGQRSGLQRALPGCCGKDQVERDAGAQHADQEVDHRHLPTADLA\n/ // ID transeq-ex7 UC To translate a specific set of regions corresponding to a known set of coding sequences: AP transeq CL tembl:x13776 amir.pep -reg=2-45,67-201,328-509 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI amir.pep FZ = 209 FP /^>X13776_1/ FP /^VRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLRVFAEHRLRRSGAE\n/ FP /^X\Z/ // ID transeq-ex8 UC To translate a mitochondrial sequence using the mammalian mitochondrion genetic code table: AP transeq CL ../../data/mito.seq mito.pep -table 2 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI mito.pep FZ = 5626 FP /^>NC_001321\.1_1/ FP /^VNY\*SAHDHNMTEVSYIWYFFIFFGGLARTPLWP\*\*VSSQSDKL\*LGLDVFVIWLAQPTC\n/ // ID transeq-list0 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range0.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 1237 FP /^LFSVVAAVPEIKMLLMTEKKKKKX\n/ FP /^STVTQLPTKWWPSRTSLLVRSSTPEETRPSRLTC\*PMAAASVPLSPAAHPLASTRRLSSV\n/ FP /^KKKKX\n/ // ID transeq-list1 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range1.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 733 FP /^AAGKKLPR\n/ FP /^STVTQLPTKWWPSRTSLLVRSSTPEETRPSRLTC\*PMAAASVPLSPAAHPLASTRRLSSV\n/ FP /^KKKKX\n/ // ID transeq-list2 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range2.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 1135 FP /^PAAGKKLPRLPKCARCRNHGYSSPLKGHKRFCMWRDCQCKKCSLIAERQRVMAVQVALRR\n/ FP /^LFSVVAAVPEIKMLLMTEKKKKKX\n/ FP /^MVAIKDITARQILDSRGNPTVEVDLLTDGGCFRAAVPSGASTGIYEALELRDKDQTKFMG\n/ FP /^QLMRIEESLGSDCQYAGAGFRHPN\*\n/ // ID transeq-list12 UC To translate from a list of sequences and test the ranges are set correctly AP transeq CL @../../data/range12.list list.pep FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI list.pep FZ = 631 FP /^AAGKKLPR\n/ FP /^MVAIKDITARQILDSRGNPTVEVDLLTDGGCFRAAVPSGASTGIYEALELRDKDQTKFMG\n/ FP /^QLMRIEESLGSDCQYAGAGFRHPN\*\n/ // ID trimest-ex AP trimest CL tembl:x65923 x65923.seq FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.seq FZ = 575 FP /poly-A tail removed/ // ID trimseq-ex AP trimseq CL ../../data/untrimmed.seq trim1.seq -window 1 -percent 100 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI trim1.seq FZ = 528 FP /^>myseq/ FP /^ttyyyctttctcgactc/ FP /ttca-gnntcy\n/ // ID trimseq-ex2 AP trimseq CL ../../data/untrimmed.seq trim2.seq -window 5 -percent 40 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI trim2.seq FZ = 523 FP /^>myseq/ FP /^ttyyyctttctcgactc/ FP /ttca-g\n/ // ID trimseq-ex3 AP trimseq CL ../../data/untrimmed.seq trim3.seq -window 5 -percent 50 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI trim3.seq FZ = 528 FP /^>myseq/ FP /^ttyyyctttctcgactc/ FP /ttca-gnntcy\n/ // ID trimseq-ex4 AP trimseq CL ../../data/untrimmed.seq trim4.seq -window 5 -percent 50 -strict FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI trim4.seq FZ = 522 FP /^>myseq/ FP /^ctttctcgactc/ FP /ttca-gnntc\n/ // ID trimseq-ex5 AP trimseq CL ../../data/untrimmed.seq trim5.seq -window 5 -percent 50 -strict -noright FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI trim5.seq FZ = 529 FP /^>myseq/ FP /^ctttctcgactc/ FP /ttca-gnntcynnnnnn\n/ // ID trimspace-ex AP trimspace IN ../../data/seqspace2.txt IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI seqspace2.trimspace FC = 46 FP /^>X13776 Pseudomonas aeruginosa amiC and amiR gene\n/ FP /^ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga\n/ // ID twofeat-ex UC Without the -twoout option the output report contains just one feature UC for every pair of features found. AP twofeat CL tembl:x65923 IN polyA_signal IN polyA_site IN 10 IN 50 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.twofeat FZ = 842 FP /484 509 [+] 0\.000 484 489 509 509/ FP /^# Reported_sequences: 1\n/ FP /^# Reported_hitcount: 1\n/ // ID twofeat-ex2 UC The -twoout option makes the output report give the pairs of features found. The output report format type has been changed to display the full original pairs of features in GFF format. AP twofeat CL -twoout -rformat gff tembl:x65923 IN polyA_signal IN polyA_site IN 10 IN 50 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65923.twofeat FZ = 217 FP /polyA_signal_sequence\t484\t489/ // ID urlget-ex AP urlget CL pseudocap:PA3363 -swiss IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pa3363.url FC = 1 FP 1 /^http:\/\/www\.pseudomonas\.com\/getAnnotation\.do\?locusID\=PA3363 Locus ID \(PseudoCAP\): PA3363\n/ // ID urlget-noswiss AP urlget CL pseudocap:PA3363 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pa3363.url FC = 2 FP 1 /^http:\/\/www\.pseudomonas\.com\/getAnnotation\.do\?locusID\=PA3363 Locus ID \(PseudoCAP\): PA3363\n/ // ID urlget-id AP urlget CL pseudocap:PA3363 -identifier "Locus ID (PseudoCAP)" IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI pa3363.url FC = 1 FP 1 /^http:\/\/www\.pseudomonas\.com\/getAnnotation\.do\?locusID\=PA3363 Locus ID \(PseudoCAP\): PA3363\n/ // ID union-ex UC The file 'cds.list' contains a list of the regions making up the coding sequence of 'embl:x65923': AP union IN @../../data/cds.list IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x65921.fasta FZ = 447 FP 1 /^>/ // ID vectorstrip-ex AP vectorstrip CL @../../data/vecseqs.list IN IN ../../data/vectors IN IN IN vector.strip IN vector.fasta FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI vector.strip FZ = 1835 FP /tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca/ FI vector.fasta FZ = 457 FP /tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca/ // ID water-ex AP water CL tsw:hba_human tsw:hbb_human IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.water FZ > 1175 FP /^# Score: 293\.5\n/ FP /^HBA_HUMAN +3 +LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS- +50\n/ FP /^HBB_HUMAN +4 +LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST +51\n/ FP /^HBA_HUMAN +51 +----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP +96\n/ FP /^# Identity: +63/145 \(43\.4%\)\n/ FP /^# Similarity: +88/145 \(60\.7%\)\n/ // ID water-gapafterfirstresidue AP water CL asis:catt asis:cgatt stdout -auto -gapopen 1 -gapextend 1 FI stdout FZ > 15 FP /# Score: 19/ FP /.*c-att/ FP /.*cgatt/ // ID whichdb-ex AP whichdb PP EMBOSS_RCHOME=N PP export EMBOSS_RCHOME TI 300 CL -showall IN x65921 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.whichdb FZ > 0 FP /^tembl:x65921\n/ // ID wobble-ex UC Here is a sample session with wobble. The example sequence is from UC Pseudomonas aeruginosa, which has a high G+C content and a very biased UC third codon position (if it can be G or C, it usually is). AP wobble IN tembl:x13776 IN cps IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 18 FP /^Created wobble\.ps\n/ FI x13776.wobble FZ = 46 FP /^Expected GC content in third position = 66\.54\n/ FI wobble.ps FC = 1749 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID wordcount-ex AP wordcount CL tembl:u68037 -wordsize=3 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI u68037.wordcount FZ = 432 FP /\Actg\s+54\n/ FP /^aaa\s+1\Z/ // ID wordfinder-ex TI 400 AP wordfinder CL tembl:j01636 @../../data/eclac.list -word 50 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI wordfinder.error FC = 5 FP 5 /^Target [0-9]+ [A-Z][0-9]+ matches 1\n/ FI j01636.wordfinder FZ > 71230 FP /^J01636 +1 / FP /^# Score: 37385\.0/ FP 5 /^# Score: / FP /^X51872 +1801 [acgt]+ +1832\n/ // ID wordmatch-ex AP wordmatch CL tsw:hba_human tsw:hbb_human IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP /^ +5 HBA_HUMAN +[+] +59\.\.63 +HBB_HUMAN +[+] +64\.\.68\n/ FP /^ +4 HBA_HUMAN +[+] +15\.\.18 +HBB_HUMAN +[+] +16\.\.19\n/ FP /^ +4 HBA_HUMAN +[+] +117\.\.120 +HBB_HUMAN +[+] +122\.\.125\n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /Number of patterns\/words found: 139/ // ID wossdata-ex UC Search for programs with 'codon' in their input, output or parameters AP wossdata CL codon FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 10 /^[a-z]\S+ / FP /^cai / FP /^chips / FP /^cusp / FP /^cutgextract / FP 0 /seqret / FC = 12 // ID wossinput-ex UC Search for programs with 'codon' in their input: AP wossinput CL codon FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 8 /^[a-z]\S+ / FP /^cai / FP /^cutgextract / FP 0 /^chips / FP 0 /^cusp / FP 0 /seqret / FC = 10 // ID wossname-ex UC Search for programs with 'restrict' in their description: AP wossname CL restrict FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^recoder / FP /^remap / FP /^restover / FP /^silent / FP 0 /seqret / // ID wossname-ex2 UC Display a listing of programs in their groups: AP wossname CL -search "" FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^recoder / FP /^remap / FP /^restover / FP /^silent / FP /^seqret / FP /^DATA RESOURCES/ // ID wossname-ex3 UC Display an alphabetic listing of all programs: AP wossname CL -search "" -alphabetic FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP s /\AALPHABETIC.*\naaindexextract / // ID wossname-ex4 UC Display only the groups that the programs can belong to: AP wossname CL -search "" -groups FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^[A-Z]/ FP 0 /^[^A-Z]/ // ID wossname-ex5 UC Output html tags around the list of programs: AP wossname CL "" -html -out wossname.html FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI wossname.html FP /AFULL \.\.\nAACCGG\n/ FP 1 /^>BFULL \.\.\nAACGGG\n/ FC = 43 // ID align-matcher-markx10 AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -aformat markx10 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^>AFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nAACCGG\n/ FP 1 /^>BFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nAACGGG\n/ FC = 64 // ID align-matcher-fasta AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -aformat fasta IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^>AFULL\n/ FP 1 /^AACCGG\n/ FP 1 /^>BFULL\n/ FP 1 /^AACGGG\n/ FC = 4 // ID align-matcher-msf AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -aformat msf IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^AFULL +AACCGG\n/ FP 1 /^BFULL +AACGGG\n/ FC = 13 // ID align-matcher-msfall AP matcher CL -gapopen 5 -gapextend 1 -stdout CL -aformat msf IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^AFULL +AAACCCGGG\.\.TTT\n/ FP 1 /^BFULL +AAAC\.\.GGGCCTTT\n/ FC = 13 // ID align-matcher-fullrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\n/ FP 1 /^ 20 \n/ FP 1 /^ AFULL AAA--CCCGGGTTT\n/ FP 1 /^ BFULL AAAGGCCCG--TTT\n/ FP 1 /^ 10 \n/ FC = 42 // ID align-matcher-partrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +46\/64 \(71\.9%\)/ FP /^# Score: +196\n/ FP 1 /^ 50 40 30 20 \n/ FP 1 /^ 50 40 30 20 \n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL GGGTTTAACCGGTT\n/ FP 1 /^ APART GGGTTTAACCGGTT\n/ FP 1 /^ 10 \n/ FC = 48 // ID align-matcher-beginrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\n/ FP 1 /^ 20 \n/ FP 1 /^ AFULL AAA--CCCGGGTTT\n/ FP 1 /^ BFULL AAAGGCCCG--TTT\n/ FP 1 /^ 10 \n/ FC = 43 // ID align-matcher-endrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -send1 15 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/10 \(70\.0%\)/ FP /^# Score: +25\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL AA--CCGGTT\n/ FP 1 /^ BFULL AAGGCCCGTT\n/ FP 1 /^ 10 \n/ FC = 43 // ID align-matcher-begin2rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin2 5 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/9 \(77\.8%\)/ FP /^# Score: +29\n/ FP 1 /^ 50\n/ FP 1 /^ AFULL AATTGGCCC\n/ FP 1 /^ BFULL AA--GGCCC\n/ FP 1 /^ 10 \n/ FC = 43 // ID align-matcher-end2rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -send2 -3 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/11 \(72\.7%\)/ FP /^# Score: +30\n/ FP /^ 50 \n/ FP /^ AFULL GGCCCAAATTT\n/ FP /^ BFULL GGCCCG--TTT\n/ FP /^ 1\n/ FC = 43 // ID align-matcher-begendallrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP /^ 10 \n/ FP /^ AFULL CCGGTT\n/ FP /^ BFULL CCCGTT\n/ FP /^ 2\n/ FC = 46 // ID align-matcher-pairrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat pair IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP 1 /^AFULL +10 CCGGTT +5\n/ FP 1 /^BFULL +7 CCCGTT +2\n/ FC = 45 // ID align-matcher-srspairrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat srspair IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP 1 /^AFULL +10 CCGGTT +5\n/ FP 1 /^BFULL +7 CCCGTT +2\n/ FC = 45 // ID align-matcher-markx0rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat markx0 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL CCGGTT\n/ FP 1 /^ :: :::\n/ FP 1 /^ BFULL CCCGTT\n/ FP 1 /^ 2\n/ FC = 47 // ID align-matcher-markx1rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat markx1 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL CCGGTT\n/ FP 1 /^ X \n/ FP 1 /^ BFULL CCCGTT\n/ FP 1 /^ 2\n/ FC = 47 // ID align-matcher-markx2rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat markx2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL CCGGTT\n/ FP 1 /^ BFULL \.\.C\.\.\.\n/ FC = 45 // ID align-matcher-markx3rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat markx3 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\n/ FP 1 /^>AFULL \.\.\nCCGGTT\n/ FP 1 /^>BFULL \.\.\nCCCGTT\n/ FC = 45 // ID align-matcher-markx10rev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat markx10 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^>AFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nCCGGTT\n/ FP 1 /^>BFULL \.\.\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\n;[^\n]+\nCCCGTT\n/ FC = 66 // ID align-matcher-fastarev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat fasta IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^>AFULL\n/ FP 1 /^CCGGTT\n/ FP 1 /^>BFULL\n/ FP 1 /^CCCGTT\n/ FC = 4 // ID align-matcher-msfrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 CL -aformat msf IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^AFULL +CCGGTT\n/ FP 1 /^BFULL +CCCGTT\n/ FC = 13 // ID align-matcher-msfallrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -srev1 -srev2 CL -aformat msf IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP 1 /^AFULL +AAA\.\.CCCGGGTTT\n/ FP 1 /^BFULL +AAAGGCCCG\.\.TTT\n/ FC = 13 // ID align-matcherprot-full AP matcher CL -stdout IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +198\n/ FP 1 /^ 60 70\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: \. :::::\.:\.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 44 // ID align-matcherprot-begin AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +195\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: \. :::::\.:\.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 47 // ID align-matcherprot-end AP matcher CL -stdout -send1 15 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/13 \(61\.5%\)/ FP /^# Score: +42\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL FIAAEEFLFIIAA\n/ FP 1 /^ ::::\.\.: \.:::\n/ FP 1 /^ BFULL FIAADDFFILIAA\n/ FP 1 /^ 10 \n/ FC = 39 // ID align-matcherprot-begin2 AP matcher CL -stdout -sbegin2 5 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +36\/64 \(56\.[23]%\)/ FP /^# Score: +180\n/ FP 1 /^ AFULL IAALEEFFIIAEFL\n/ FP 1 /^ ::: \. :::::\.:\.\n/ FP 1 /^ BFULL IAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 45 // ID align-matcherprot-end2 AP matcher CL -stdout -send2 -3 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +198\n/ FP 1 /^ 60 70\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: \. :::::\.:\.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 45 // ID align-matcherprot-begendall AP matcher CL -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/11 \(54\.5%\)/ FP /^# Score: +32\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL AAEEFLFIIAA\n/ FP 1 /^ BFULL AADDFFILIAA\n/ FP 1 /^ 10 \n/ FC = 42 // ID align-matcherprot-fullrev AP matcher CL -stdout -srev1 -srev2 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +198\n/ FP 1 /^ 60 70\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: \. :::::\.:\.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 46 // ID align-matcherprot-beginrev AP matcher CL -gapopen 5 -gapextend 1 -stdout -sbegin1 5 -srev1 -srev2 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +195\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: \. :::::\.:\.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 49 // ID align-matcherprot-endrev AP matcher CL -stdout -send1 15 -srev1 -srev2 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/13 \(61\.5%\)/ FP /^# Score: +42\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL FIAAEEFLFIIAA\n/ FP 1 /^ ::::\.\.: \.:::\n/ FP 1 /^ BFULL FIAADDFFILIAA\n/ FP 1 /^ 10 \n/ FC = 41 // ID align-matcherprot-begin2rev AP matcher CL -stdout -sbegin2 5 -srev1 -srev2 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +36\/64 \(56\.[23]%\)/ FP /^# Score: +180\n/ FP 1 /^ AFULL IAALEEFFIIAEFL\n/ FP 1 /^ ::: \. :::::\.:\.\n/ FP 1 /^ BFULL IAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 47 // ID align-matcherprot-end2rev AP matcher CL -stdout -send2 -3 -srev1 -srev2 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +40\/68 \(58\.8%\)/ FP /^# Score: +198\n/ FP 1 /^ 60 70\n/ FP 1 /^ AFULL FFIIIAALEEFFIIAEFL\n/ FP 1 /^ ::::::: \. :::::\.:\.\n/ FP 1 /^ BFULL FFIIIAADDLFFIIADFI\n/ FP 1 /^ 60 \n/ FC = 47 // ID align-matcherprot-begendallrev AP matcher CL -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 -srev1 -srev2 IN ../../data/aligna.prot IN ../../data/alignb.prot IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/11 \(54\.5%\)/ FP /^# Score: +32\n/ FP 1 /^ 10 \n/ FP 1 /^ AFULL AAEEFLFIIAA\n/ FP 1 /^ BFULL AADDFFILIAA\n/ FP 1 /^ 10 \n/ FC = 44 // ID align-wordmatch-same AP wordmatch CL tembl:v00294 tembl:v00294 -word 50 -auto FI v00294.wordmatch FC = 23 FP /^ +1113 +V00294 +[+] +1\.\.1113 +V00294 +[+] +1\.\.1113\n/ FI V00294.gff FZ = 184 FP /^V00294\twordmatch\tsequence_feature\t1\t1113\t1\.000\t/ FI wordmatch.log FP /Number of patterns\/words found: 1064/ FP /Sum of match lengths: 1113/ // ID align-wordmatch-pair AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat pair IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HUMAN 59 HGKKV 63\n/ FP 1 /^ \|\|\|\|\|\n/ FP 2 /^ \|\|\|\|\n/ FP 1 /^HBB_HUMAN 64 HGKKV 68\n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /Number of all matches: 3/ // ID align-wordmatch-srspair AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat srspair IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HUMAN 59 HGKKV 63\n/ FP 1 /^ \|\|\|\|\|\n/ FP 2 /^ \|\|\|\|\n/ FP 1 /^HBB_HUMAN 64 HGKKV 68\n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /^EFTP/ FP /^HGKK/ // ID align-wordmatch-markx0 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx0 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HU HGKKV\n/ FP 1 /^ :::::\n/ FP 1 /^HBB_HU HGKKV\n/ FP 1 /^ 60 \n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /^WGKV/ // ID align-wordmatch-markx1 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx1 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^HBA_HU HGKKV\n/ ## found for numbering and for alignment in first hit FP 2 /^ \n/ FP 1 /^HBB_HU HGKKV\n/ FP 1 /^ 60 \n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /^HGKK.*5.0/ // ID align-wordmatch-markx2 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx2 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^ 60 \n/ FP 1 /^HBA_HU HGKKV\n/ FP 1 /^HBB_HU -----\n/ FP 2 /^HBB_HU ----\n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /Average match length: 4.33/ // ID align-wordmatch-markx3 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx3 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 1 /^>HBA_HUMAN \.\.\nHGKKV\n/ FP 1 /^>HBB_HUMAN \.\.\nHGKKV\n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /^EFTP.*4.0/ // ID align-wordmatch-markx10 AP wordmatch CL tsw:hba_human tsw:hbb_human -aformat markx10 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI hba_human.wordmatch FZ > 608 FP 3 /^>HBA_HUMAN \.\.\n/ FP 3 /^; sq_len: 142\n/ FP 1 /^; al_start: 59\n/ FP 1 /^; al_stop: 63\n/ FP 1 /^; al_display_start: 59\n/ FP 2 /^HGKKV\n/ FP 3 /^>HBB_HUMAN \.\.\n/ FP 3 /^; sq_len: 147\n/ FP 1 /^; al_start: 64\n/ FP 1 /^; al_stop: 68\n/ FP 1 /^; al_display_start: 64\n/ FI HBA_HUMAN.gff FZ = 372 FP /^HBA_HUMAN\twordmatch\tpolypeptide_region\t59\t63\t1\.000\t/ FI HBB_HUMAN.gff FZ = 372 FP /^HBB_HUMAN\twordmatch\tpolypeptide_region\t64\t68\t1\.000\t/ FI wordmatch.log FP /^HGKK.*5.0/ // ID align-merger-fasta AP merger CL -aformat fasta IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 108 FP /accggaaaaaaga\n[-]+\n/ FP /^---------------------gtgaatgaagtcgcttaagcaatcaatgtcggatgcggc\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx0 AP merger CL -aformat markx0 IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 421 FP /^# Score: 795\.0\n/ FP / 1340 1350\nV00295 cgctt/ FP /^V00295 cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^X51872 [-]+gtgaatgaa\n +\n/ FP /^X51872 .*tccgaccaac\n 10/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx1 AP merger CL -aformat markx1 IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 421 FP /^# Score: 795\.0\n/ FP / 1340 1350\nV00295 cgctt/ FP /^V00295 cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^X51872 [-]+gtgaatgaa\n +\n/ FP /^X51872 .*tccgaccaac\n 10/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx2 AP merger CL -aformat markx2 IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 293 FP /^# Score: 795\.0\n/ FP / 1340 1350\nV00295 cgctt/ FP /^V00295 cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^V00295 [acgt]+gtgaatgaa\nX51872 [-]+\.\.\.\.\.\.\.\.\.\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx3 AP merger CL -aformat markx3 IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 167 FP /^# Score: 795\.0\n/ FP /^cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^-----------------------------------------gtgaatgaa\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-markx10 AP merger CL -aformat markx10 IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 188 FP /^; sw_score: 795\.0\n/ FP /^cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^-----------------------------------------gtgaatgaa\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-match AP merger CL -aformat match IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 30 FP /^ 159 V00295 +[+] +1342\.\.1500 X51872 +[+] +1\.\.159\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-msf AP merger CL -af msf IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 265 FP /^V00295 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa\n/ FP /^X51872 +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gtgaatgaa\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-pair AP merger CL -aformat pair IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FZ > 1445 FP /^# Score: 795\.0\n/ FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^X51872 +1 [-]+gtgaatgaa +9\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-score AP merger CL -aformat score IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 9 FP 0 /^# Score:/ FP /^V00295 X51872 3173 \(795\.0\)\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-simple AP merger CL -aformat simple IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 293 FP /^# Score: 795\.0\n/ FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^X51872 +1 [-]+gtgaatgaa +9\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-srs AP merger CL -aformat srs IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 229 FP /^# Score: 795\.0\n/ FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^X51872 +1 [-]+gtgaatgaa +9\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-srspair AP merger CL -aformat srspair IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 293 FP /^# Score: 795\.0\n/ FP /^V00295 +1301 +cgcttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaa +1350\n/ FP /^X51872 +1 [-]+gtgaatgaa +9\n/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-merger-tcoffee AP merger CL -aformat tcoffee IN tembl:v00295 IN tembl:x51872 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00295.merger FC = 167 FP /^2\nV00295 1500 ttccagct/ FP /^! score=795\.0\n/ FP /^1342 1 0 1 0\n/ FP /^1500 159 0 1 0\n/ FP 0 /^1501/ FI v00295.fasta FC = 54 FZ = 3291 FP 1 /^>/ FP /^agcttccggccagcgccagcccgcccatggtaaccaccggcagagcggtcgac\n/ FP /ggaaaaaaga\ncttcgtggg/ // ID align-needle-full AP needle CL -gapopen 16 -gapext 4 -stdout IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/64 \(12\.5%\)/ FP /^# Score: +24\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg 50\n/ FP 1 /^ + \|\|\|\|\.\.\|\.\.\|\|\| \n/ FP 1 /^BFULL +1 ------------aaacgggccttt-------------------------- 12\n/ FC = 42 // ID align-needle-part AP needle CL -gapopen 16 -gapext 4 -stdout IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +46\/67 \(68\.7%\)/ FP /^# Score: +162\.0\n/ FP 1 /^AFULL 48 ttgggccaattggcatg 64\n/ FP 1 /^ \|\| \.\.\|\|\.\.\|\| \n/ FP 1 /^APART 47 tt-aaccggtt------ 56\n/ FC = 42 // ID align-needle-begin AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/60 \(13\.3%\)/ FP /^# Score: +24\.0\n/ FP 1 /^AFULL +5 aaccggttaaacccgggtttaaaaccccggggttttcccaaatttgggcc 54\n/ FP 1 /^ + \|\|\|\|\.\.\|\.\.\|\|\| +\n/ FP 1 /^BFULL +1 --------aaacgggccttt------------------------------ 12\n/ FP 1 /^BFULL +12 ---------- 12\n/ FC = 43 // ID align-needle-end AP needle CL -gapopen 16 -gapext 4 -stdout -send1 15 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +3\/24 \(12\.5%\)/ FP /^# Score: +15\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaa--------- 15\n/ FP 1 /^BFULL +1 ------------aaacgggccttt 12\n/ FC = 39 // ID align-needle-begin2 AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin2 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/64 \( 9\.4%\)/ FP /^# Score: +22\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg 50\n/ FP 1 /^BFULL +5 --------------------------------gggccttt---------- 12\n/ FC = 43 // ID align-needle-end2 AP needle CL -gapopen 16 -gapext 4 -stdout -send2 -3 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/64 \( 9\.4%\)/ FP /^# Score: +14\.0\n/ FP 1 /^AFULL +1 acgtaaccggttaaacccgggtttaaaaccccggggttttcccaaatttg 50\n/ FP 1 /^BFULL +1 ------------aaacgggcct---------------------------- 10\n/ FC = 43 // ID align-needle-begendall AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/11 \(45\.5%\)/ FP /^# Score: +21\.0\n/ FP 1 /^AFULL +5 aaccggttaaa 15\n/ FP 1 /^BFULL +2 aacggg----- 7\n/ FC = 42 // ID align-needle-fullrev AP needle CL -gapopen 16 -gapext 4 -stdout -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/64 \(12\.5%\)/ FP /^# Score: +24\.0\n/ FP /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt 15\n/ FP /^ + \|\|\|\.\.\|\.\.\|\|\n/ FP /^BFULL +12 ----------------------------------------aaaggcccgt 3\n/ FC = 44 // ID align-needle-partrev AP needle CL -gapopen 16 -gapext 4 -stdout -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +4[4,6]\/6[6,7] \(6[6,8]\.7%\)/ FP /^# Score: +162\.0\n/ FP /^AFULL +1[6,7] g+tttaaccggttacgt 1\n/ FP /^ + [\|]{10,13} \n/ FP /^APART +1[2,3] g+tttaaccggtt---- 1\n/ FC = 44 // ID align-needle-beginrev AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/60 \(13\.3%\)/ FP /^# Score: +24\.0\n/ FP 1 /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt 15\n/ FP 1 /^ + \|\|\|\.\.\|\.\.\|\|\n/ FP 1 /^BFULL +12 ----------------------------------------aaaggcccgt 3\n/ FC = 45 // ID align-needle-endrev AP needle CL -gapopen 16 -gapext 4 -stdout -send1 15 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +3\/24 \(12\.5%\)/ FP /^# Score: +15\.0\n/ FP 1 /^AFULL +15 ---------tttaaccggttacgt 1\n/ FP 1 /^BFULL +12 aaaggcccgttt------------ 1\n/ FC = 41 // ID align-needle-begin2rev AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin2 5 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/64 \( 9\.4%\)/ FP /^# Score: +22\.0\n/ FP /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt 15\n/ FP /^BFULL +12 -------aaaggccc----------------------------------- 5\n/ FC = 45 // ID align-needle-end2rev AP needle CL -gapopen 16 -gapext 4 -stdout -send2 -3 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/64 \( 9\.4%\)/ FP /^# Score: +14\.0\n/ FP /^AFULL +64 catgccaattggcccaaatttgggaaaaccccggggttttaaacccgggt 15\n/ FP /^BFULL +10 -aggcccgttt--------------------------------------- 1\n/ FC = 45 // ID align-needle-begendallrev AP needle CL -gapopen 16 -gapext 4 -stdout -sbegin1 5 -send1 15 CL -sbegin2 2 -send2 -6 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/11 \(45\.5%\)/ FP /^# Score: +21\.0\n/ FP /^AFULL +15 tttaaccggtt 5\n/ FP /^BFULL +7 -----cccgtt 2\n/ FC = 44 // ID needle-noendweight AP needle CL -gapopen=8 -gapextend=8 -stdout -datafile=EBLOSUM50 -endweight=no IN asis::PAWHEAE IN asis::HEAGAWGHEE IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +4\/11 \(36\.4%\)/ FP /^# Score: +25\.0\n/ FP /^asis 1 ---PAW-HEAE 7\n/ FP /^asis 1 HEAGAWGHEE- 10\n/ FC = 40 // ID needle-endweight1 AP needle CL -gapopen=8 -gapextend=8 -endopen=8 -endextend=8 -stdout CL -datafile=EBLOSUM50 -endweight IN asis::PAWHEAE IN asis::HEAGAWGHEE IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/11 \(45\.5%\)/ FP /^# Score: +1\.0\n/ FP /^asis 1 -(-P)|(P-)|(PA)-(A)|(-)W-HEAE 7\n/ FP /^asis 1 HEAGAWGHE-E 10\n/ FC = 42 // ID needle-endweight2 AP needle CL asis:actggatatataatat asis:actaatat stdout -auto -endweight CL -gapopen 20 FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/16/ FP /^# Score: +16\.5/ FP /^asis +1 ac--------taatat/ FC = 39 // ID needle-endweight3 AP needle CL asis:actggatatataatat asis:actaatat stdout -auto -endweight CL -gapopen 20 -gapextend 2 -endextend 1 FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/16/ FP /^# Score: +6\.0/ FP /^asis +1 ac--------taatat/ FC = 41 // ID needle-endweight4 AP needle CL asis:actggatatataatat asis:actaatat stdout -auto -endweight CL -gapopen 20 -gapextend 2 -endextend 0 FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +6\/16/ FP /^# Score: +12\.0/ FP /^asis +1 --------actaatat/ FC = 41 // ID needle-endweight5 AP needle CL asis:MVL asis:MVHLLL stdout -aformat simple -endweight -auto CL -gapopen 12 -gapextend 2 FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +3\/6/ FP /^# Score: +-3\.0/ FP /^asis +1 MV---L / FC = 41 // ID needle-endweight6 AP needle CL asis:MGQMQIV asis:IVPPLKP stdout -aformat simple -endweight -auto CL -endopen 0 -endextend 0 FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +2\/12/ FP /^# Score: +8\.0/ FP /^asis +1 -----IVPPLKP / FC = 41 // ID needle-endweight7 AP needle CL asis:IVPPLKP asis:MGQMQIV stdout -aformat simple -endweight -auto CL -endopen 0 -endextend 0 FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +2\/12/ FP /^# Score: +8\.0/ FP /^asis +1 MGQMQIV----- / FC = 41 // ID needle-traceback1 AP needle CL -auto -stdout -aformat simple -gapextend 1.0 CL asis::acgtaggtacgttttacgtacgtacgtacgtaaacaggtg CL asis::acgtagaacgtacgtacgtacgtacacgcataagcggcag FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +28\/48 \(58\.3%\)/ FP /^# Score: +94\.0\n/ FP /^asis +1 acgtaggtacgttttacgtacgtacgtacgtaaac----aggtg---- 40\n/ FP /^asis +1 acgtag--------aacgtacgtacgtacgtacacgcataagcggcag 40\n/ FC = 39 // ID needle-traceback2 AP needle CL -auto -stdout -aformat simple -gapextend 0.5 CL asis::tgcgcaggatgtccttccaa CL asis::caatagactggtccgttcgc FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +12\/28 \(42\.9%\)/ FP /^# Score: +17\.0\n/ FP /^asis +1 tgcgcaggat------gtcc-ttc-caa/ FP /^asis +1 ----ca--atagactggtccgttcgc--/ FC = 39 // ID needle-traceback3 AP needle CL -auto -stdout CL asis::CDISRILQTHADAKVQVLDNQNVSNGCVSKILGRYYETG CL asis::CDISRILQ--------------VSNGCVSKILGRYYETG FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +25\/39 \(64\.1%\)/ FP /^# Score: +115\.5\n/ FP /^asis +1 CDISRILQTHADAKVQVLDNQNVSNGCVSKILGRYYETG/ FP /^asis +1 CDISRILQ--------------VSNGCVSKILGRYYETG/ FC = 37 // ID needle-indel AP needle CL asis:cttttcgtggtatta asis:gcgaccatgagagag CL -auto -gapo 1 -gape 1 -endw -endo 1 -ende 1 stdout FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/23 \(30\.4%\)/ FP /^# Gaps: +16\/23 \(69\.6%\)/ FP /^# Score: +19\.0\n/ FP /^asis +1 (ctttt-)|(-ctttt)cg----tg-gta[ta-]{5}/ FP / +|| || | | |/ FP /^asis +1 (-----g)|(g-----)cgaccatgag-a[ga-]{5}/ FC = 42 // ID needle-simple1 AP needle CL asis:aag asis:gg stdout -auto -endw FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +1\/3 \(33\.3%\)/ FP /^# Gaps: +1\/3 \(33\.3%\)/ FP /^# Score: +-9\.0\n/ FP /^asis +1 aag/ FP / + \.|/ FP /^asis +1 -gg/ FC = 38 // ID needle-simple2 AP needle CL asis:aa asis:gg stdout -auto FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +0\/4 \( 0\.0%\)/ FP /^# Similarity: +0\/4 \( 0\.0%\)/ FP /^# Score: 0\.0\n/ FP /^asis +1 aa--/ FP /^asis +1 --gg/ FC = 37 // ID needleall-withendweight AP needleall CL -auto -stdout -endweight -aformat simple CL asis::DVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFV\ CL FYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEV CL asis::RDDEERPMILIAGGTGFSYARSILLTALARNPNRDITIYWGGREEQHLYDLCELEALSLKHPGLQVV\ CL PVVEQPEAGWRGRTGTVLTAVLQDHGTLAEHDIYIAGRFEMAKIARDLFCSERNAREDRLFGDA FI needleall.error FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +32\/155 \(20\.6%\)/ FP /^# Score: +62\.5\n/ FP /^asis +43 ----REEQHLYDLCEL------------EALSLKHPGLQVVPVVEQPEAG/ FP /^asis +96 ------SIL---------LPDADYYICGPIPFMRMQHDAL-KNLGIHEAR/ FC = 51 // ID needleall-noendweight AP needleall CL -auto -stdout -noendweight CL asis::DVDAKTPIVLISGGVGLTPMVSMLKVALQAPPRQVVFVHGARNSAVHAMRDRLREAAKTYENLDLFV\ CL FYDQPLPEDVQGRDYDYPGLVDVKQIEKSILLPDADYYICGPIPFMRMQHDALKNLGIHEARIHYEV CL asis::RDDEERPMILIAGGTGFSYARSILLTALARNPNRDITIYWGGREEQHLYDLCELEALSLKHPGLQVV\ CL PVVEQPEAGWRGRTGTVLTAVLQDHGTLAEHDIYIAGRFEMAKIARDLFCSERNAREDRLFGDA FI needleall.error FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^asis asis 156 \(63.5\)\n/ FC = 4 // ID align-wordfinder-sam AP wordfinder CL -lowmatch 7 -stdout -auto -aformat sam -sformat2 fastq-sanger CL ../../data/illumina_adapter_primer.fa CL ../../data/test1_illumina.fastq FI stderr FI wordfinder.error FP /Target 7 FC12044_91407_8_200_10_437 matches 4/ FC = 70 FI stdout FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FC = 23 FP /_8_200_303_427.*_DpnII_Gex_Adapters1_2\t8.*6H11M.*XXXIXFQXXXO.*NM:i:2/ // ID align-wordmatch-sam AP wordmatch CL -wordsize 7 -stdout -auto -aformat sam -sformat2 fastq-sanger CL ../../data/illumina_adapter_primer.fa -nodumpfeat CL ../../data/test1_illumina.fastq FI stderr FI wordmatch.log FP /Average match length: 7.38/ FC = 32 FI stdout FP /^FC12044_91407_8_200_10_437.*CTGCTTG SXSXXXX AS:i:7 NM:i:0/ FI Illumina_Genomici_DNA_Adapters1_1.gff FC = 0 FI FC12044_91407_8_200_406_24.gff FC = 0 // ID align-supermatcher-sam AP supermatcher CL -word 7 -stdout -auto -aformat sam -sformat1 fastq-sanger CL ../../data/test1_illumina.fastq CL ../../data/illumina_adapter_primer.fa FI stderr FI supermatcher.error FP /No.*start points for.*_8_200_285_136 vs .*_Small_RNA_sequencing_primer/ FC = 754 FI stdout FP /_427.*DpnII_Gex_A.*1_2.*6H7M3I9M.*CAGAGTTTTGCTCTTGTCC.*XXXIXFQXXXOIQSSXUFF/ FP /_437.*Small_RNA_3p_Adapter\t15.*1H7M.*CTGCTTG SXSXXXX AS:i:35.0 NM:i:0/ // ID align-water-sam1 UC example from SAM paper(Bioinformatics 2009 August) AP water CL -auto -aformat sam -dataf EDNASIMPLE -outf stdout -gapo 2 CL asis:AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT CL asis:TTAGATAAAGGATACTG FI stdout FP /.*\t7\t.*\t8M2I4M1D3M\t.*\tTTAGATAAAGGATACTG\t.*\tAS:i:10.5\tNM:i:0/ // ID align-water-sam2 AP water CL -auto -aformat sam -datafile EDNASIMPLE -outfile stdout CL asis:AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT CL asis:gcctaAGCTAA FI stdout FP /.*\t9\t.*\t5H6M\t.*\tAGCTAA\t.*\tAS:i:4.0\tNM:i:1/ // ID align-water-sam3 AP water CL -auto -srev2 -aformat sam -datafile EDNASIMPLE -outfile stdout CL asis:AGCATGTTAGATAANNGANAGCTGTGCTAGTAGGCAGTCAGCGCCAT CL asis:gcctaAGCTAA FI stdout FP /.*\t31\t.*\t6H5M\t.*\ttaggc\t.*\tAS:i:5.0\tNM:i:0/ // ID align-water-full AP water CL -gapopen 5 -gapext 1 -stdout IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\.0\n/ FP 1 /^AFULL 13 aaacccggg--ttt 24\n/ FP 1 /^BFULL 1 aaa--cgggccttt 12\n/ FC = 38 // ID align-water-part AP water CL -gapopen 5 -gapext 1 -stdout IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +46\/62 \(74\.2%\)/ FP /^# Score: +196\.0\n/ FP 1 /^AFULL +5 aaccggttaaacccgggtttaaaaccccggggtttt---cccaaatttgg 51\n/ FP 1 /^APART +1 aaccggttaaacccgggtttaaaaccccggggttttaaaccc------gg 44\n/ FC = 42 // ID align-water-begin AP water CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\.0\n/ FP 1 /^AFULL 13 aaacccggg--ttt 24\n/ FP 1 /^BFULL 1 aaa--cgggccttt 12\n/ FC = 39 // ID align-water-end AP water CL -gapopen 5 -gapext 1 -stdout -send1 15 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/10 \(70\.0%\)/ FP /^# Score: +25\.0\n/ FP 1 /^AFULL 5 aaccgg--tt 12\n/ FP 1 /^BFULL 2 aacgggcctt 11\n/ FC = 39 // ID align-water-begin2 AP water CL -gapopen 5 -gapext 1 -stdout -sbegin2 5 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/9 \(77\.8%\)/ FP /^# Score: +29\.0\n/ FP 1 /^AFULL 50 gggccaatt 58\n/ FP 1 /^BFULL 5 gggcc--tt 11\n/ FC = 39 // ID align-water-end2 AP water CL -gapopen 5 -gapext 1 -stdout -send2 -3 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/11 \(72\.7%\)/ FP /^# Score: +30\.0\n/ FP 1 /^AFULL 44 aaatttgggcc 54\n/ FP 1 /^BFULL 1 aaa--cgggcc 9\n/ FC = 39 // ID align-water-begendall AP water CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\.0\n/ FP 1 /^AFULL 5 aaccgg 10\n/ FP 1 /^BFULL 2 aacggg 7\n/ FC = 42 // ID align-water-fullrev AP water CL -gapopen 5 -gapext 1 -stdout -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\.0\n/ FP /^AFULL 24 aaa--cccgggttt 13\n/ FP /^BFULL 12 aaaggccc--gttt 1\n/ FC = 40 // ID align-water-partrev AP water CL -gapopen 5 -gapext 1 -stdout -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignapart.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +46\/62 \(74\.2%\)/ FP /^# Score: +196\.0\n/ FP /^AFULL +58 aattgg-----cccaaatttggg---aaaaccccggggttttaaacccgg 17\n/ FP /^APART +56 aaccggttaaaccc------gggtttaaaaccccggggttttaaacccgg 13\n/ FC = 44 // ID align-water-beginrev AP water CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +10\/14 \(71\.4%\)/ FP /^# Score: +38\.0\n/ FP 1 /^AFULL 24 aaa--cccgggttt 13\n/ FP 1 /^BFULL 12 aaaggccc--gttt 1\n/ FC = 41 // ID align-water-endrev AP water CL -gapopen 5 -gapext 1 -stdout -send1 15 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/10 \(70\.0%\)/ FP /^# Score: +25\.0\n/ FP /^AFULL 12 aa--ccggtt 5\n/ FP /^BFULL 11 aaggcccgtt 2\n/ FC = 41 // ID align-water-begin2rev AP water CL -gapopen 5 -gapext 1 -stdout -sbegin2 5 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +7\/9 \(77\.8%\)/ FP /^# Score: +29\.0\n/ FP /^AFULL 58 aattggccc 50\n/ FP /^BFULL 11 aa--ggccc 5\n/ FC = 41 // ID align-water-end2rev AP water CL -gapopen 5 -gapext 1 -stdout -send2 -3 -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +8\/11 \(72\.7%\)/ FP /^# Score: +30\.0\n/ FP /^AFULL 54 ggcccaaattt 44\n/ FP /^BFULL 9 ggccc--gttt 1\n/ FC = 41 // ID align-water-begendallrev AP water CL -gapopen 5 -gapext 1 -stdout -sbegin1 5 -send1 15 -sbegin2 2 -send2 -6 CL -srev1 -srev2 IN ../../data/aligna.dna IN ../../data/alignb.dna IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FP /^# Identity: +5\/6 \(83\.3%\)/ FP /^# Score: +21\.0\n/ FP /^AFULL 10 ccggtt 5\n/ FP /^BFULL 7 cccgtt 2\n/ FC = 44 // ID align-wordfinder-simple AP wordfinder CL -gapopen 10 -gapextend 1 -wordlen 3 -aformat simple -outfile align.simple CL asis:GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGG asis:TCGTTT -auto FI wordfinder.error FC = 1 FP /matches 1/ FI align.simple FC = 43 FP /^# Score: 21\.0/ FP /TCGTAT/ // ID align-supermatcher-default TI 400 AP supermatcher CL @../../data/eclac.list tembl:j01636 -word 50 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI j01636.supermatcher FZ > 71230 FP /^J01636 +1 / FP /^# Score: 37385\.0/ FP 5 /^# Score: / FP /^X51872 +1801 [acgt]+ +1832\n/ // ID align-supermatcher-range TI 400 AP supermatcher CL @../../data/eclac.list tembl:j01636 -word 50 -sbegin2 101 -send2 -101 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI j01636.supermatcher FZ > 69555 FP /^J01636 +101 / FP /^# Score: 36385\.0/ FP 5 /^# Score: / FP /^X51872 +1701 [acgt]+ +1732\n/ // ID align-supermatcher-defaultrev TI 400 AP supermatcher CL @../../data/eclac.list tembl:j01636 -word 50 -srev1 -srev2 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI j01636.supermatcher FZ > 71230 FP /^# Score: 37385\.0/ FP 5 /^# Score: / FP /^X51872 +1832 [acgt]+ +1783\n/ FP /^X51872 +32 [acgt]+ +1\n/ // ID align-supermatcher-rangerev TI 400 AP supermatcher CL @../../data/eclac.list tembl:j01636 -word 50 -sbegin2 101 -send2 -101 -srev1 -srev2 IN IN 3.0 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 0 FI supermatcher.error FZ = 0 FI j01636.supermatcher FZ > 69555 FP 3 /^J01636 +7277 / FP /^# Score: 36385\.0/ FP 5 /^# Score: / FP /^X51872 +32 [acgt]+ +1\n/ FP 2 /^J01636 +127 [acgt]+ +101\n/ // ID supermatcher-simple AP supermatcher CL -gapopen 10 -gapextend 1 -wordlen 3 -aformat simple -outfile align.simple CL asis:GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGG asis:TCGTTT -auto FI supermatcher.error FZ = 0 FI align.simple FC = 41 FP /^# Score: 21\.0/ FP /TCGTAT/ // ID supermatcher-minwidth AP supermatcher CL ../../data/aligna.dna ../../data/tropomyosin.fasta CL -width 1 -gapopen 1 -gapextend 1 -aformat score -outfile align.score -auto FI supermatcher.error FP /.*BG089808.*/ FZ = 62 FI align.score FZ = 372 FP /BF056441.* 12 \(33.0\)/ FP /BE848719.* 7 \(35.0\)/ FP /BF022813.* 6 \(30.0\)/ FP /BF452255.* 6 \(30.0\)/ FP /BG147728.* 6 \(30.0\)/ FP /BI817778.* 7 \(35.0\)/ FP /AF186109.* 6 \(30.0\)/ FP /AF186110.* 9 \(36.0\)/ FP /AF310722.* 9 \(36.0\)/ FP /AF362886.* 6 \(30.0\)/ FP /AF362887.* 6 \(30.0\)/ FP /AF087679.* 6 \(30.0\)/ // ID supermatcher-minscore1 AP supermatcher CL ../../data/aligna.dna ../../data/tropomyosin.fasta -auto CL -minscore 120 -gapopen 1 -gapextend 1 -aformat score -outfile align.score FI supermatcher.error FP /.*BG089808.*/ FZ = 62 FI align.score FZ = 343 FP /BF056441.* 84 \(132.0\)/ FP /BF022813.* 88 \(128.0\)/ FP /BF452255.* 88 \(128.0\)/ FP /BG147728.* 88 \(128.0\)/ FP /AF186109.* 82 \(146.0\)/ FP /AF186110.* 83 \(151.0\)/ FP /AF310722.* 83 \(151.0\)/ FP /AF362886.* 86 \(136.0\)/ FP /AF362887.* 85 \(125.0\)/ FP /AF087679.* 82 \(146.0\)/ // ID supermatcher-minscore2 AP supermatcher CL ../../data/aligna.dna ../../data/tropomyosin.fasta -minscore 35 CL -outfile align -auto -gapextend 1 -width 12 -send2 172 -send1 50 FI supermatcher.error FP /.*BG089808/ FP /.*BG147728/ FI align FC = 88 FP /Score: 38.0/ FP /BF056441 30 tattccattgcacaatttg 48/ FP / |.|||| || ||||||/ FP /AFULL 37 ttttcc----ca-aatttg 50/ FP /Score: 40.0/ FP /BE848719 102 ggtgttaaaac 112/ FP / ||| |||||||/ FP /AFULL 20 ggt-ttaaaac 29/ FP /Score: 41.0/ FP /BI817778 1 ccgggg--taccctaa 14/ FP / |||||| |.|||.||/ FP /AFULL 31 ccggggttttcccaaa 46/ // ID supermatcher-wordlen7 AP supermatcher CL ../../data/tropomyosin.fasta ../../data/aligna.dna CL -gapextend 1 -wordlen 7 -outfile align -auto FI supermatcher.error FP /.*BG089808/ FP /.*BG147728/ FI align FZ = 2850 FP /Score: 41.0/ FP /BE848719 102 ggtgttaaaacagtactcttctggttt-----agttt 133/ FP / ||| ||||||| |....||||| |.|||/ FP /AFULL 20 ggt-ttaaaac------cccggggttttcccaaattt 49/ FP /Score: 42.0/ FP /AFULL 31 ccggggttttcccaaatttgggcc 54/ FP / |||||| |.|||.|| |||/ FP /BI817778 1 ccgggg--taccctaa-----gcc 17/ FP /Score: 55.0/ FP /.* 3 gtaacc-------ggttaaacccg-ggtttaaaaccccggggttttccca 44/ FP /.* ||.||| ||| .||| || ||||.| .|..|||./ FP /.* 740 gtgacctgaaggaggt----gccgcgg---aaaaac------atcaccct 776/ FP /AFULL 45 aatt-------tgggccaattggc 61/ FP / .||| ||||||| ||||/ FP /AF310722 852 cattcggggtctgggcca--tggc 873/ // ID wordfinder-simple AP wordfinder CL -gapopen 10 -gapextend 1 -wordlen 3 -aformat simple -outfile align.simple CL asis:GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGG asis:TCGTTT -auto FI wordfinder.error FP /.*matches 1/ FZ = 24 FI align.simple FC = 43 FP /^# Score: 21\.0/ FP /TCGTAT/ // ID wordfinder-minwidth AP wordfinder CL ../../data/tropomyosin.fasta ../../data/aligna.dna CL -width 1 -gapopen 1 -gapextend 1 -aformat score -outfile align.score -auto FI wordfinder.error FP /matches 12/ FC = 1 FI align.score FZ = 373 FP /AFULL BF056441 17 \(31.0\)/ FP /.+BE848719 11 \(37.0\)/ FP /.+BF022813 6 \(30.0\)/ FP /.+BF452255 6 \(30.0\)/ FP /.+BG147728 6 \(30.0\)/ FP /.+BI817778 7 \(35.0\)/ FP /.+AF186109 6 \(30.0\)/ FP /.+AF186110 9 \(36.0\)/ FP /.+AF310722 9 \(36.0\)/ FP /.+AF362886 6 \(30.0\)/ FP /.+AF362887 6 \(30.0\)/ FP /.+AF087679 6 \(30.0\)/ // ID wordfinder-minalignlen1 AP wordfinder CL ../../data/tropomyosin.fasta ../../data/aligna.dna -auto CL -lowalign 80 -gapopen 1 -gapextend 1 -aformat score -outfile align.score FI wordfinder.error FP /.*excludes 'BI817778'/ FC = 2 FI align.score FC = 14 FP /.+BF056441 83 \(121.0\)/ FP /.+BE848719 88 \(146.0\)/ FP /.+BF022813 88 \(128.0\)/ FP /.+BF452255 88 \(128.0\)/ FP /.+BG147728 88 \(128.0\)/ FP /.+AF186109 86 \(142.0\)/ FP /.+AF186110 83 \(151.0\)/ FP /.+AF310722 83 \(151.0\)/ FP /.+AF362886 86 \(136.0\)/ FP /.+AF362887 87 \(147.0\)/ FP /.+AF087679 86 \(142.0\)/ // ID wordfinder-minalignlen2 AP wordfinder CL ../../data/tropomyosin.fasta ../../data/aligna.dna -lowalign 10 CL -outfile align -auto -gapextend 1 -width 12 -send2 172 -send1 50 FI wordfinder.error FP /.*matches 1/ FI align FC = 44 FP /Score: 33.0/ FP /BF056441 37 ttgcacaatttg 48/ FP / ||.|..||||||/ FP /AFULL 39 ttcccaaatttg 50/ // ID wordfinder-wordlen7 AP wordfinder CL ../../data/aligna.dna ../../data/tropomyosin.fasta CL -gapextend 1 -wordlen 7 -outfile align -auto FI wordfinder.error FP /.*BE848719 matches 1/ FC = 4 FI align FC = 116 FP /Score: 35.0/ FP /AFULL 57 ttggcat 63/ FP / |||||||/ FP /BE848719 15 ttggcat 21/ // ####################################### # EMBOSS make check ####################################### ID ajtest-check AQ ajtest IN tembl:x13776 IN ../../data/globins.msf IN stdout IN abc.seq IN abc.gff FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI kim1.out FZ = 4629 FP /^ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP\.\n/ FI abc.seq FC = 0 FI abc.gff FC = 0 // ID ajtest-all-check AQ ajtest CL -nostdout -outfile "" CL -outseq outseq IN tembl:x13776 IN ../../data/globins.msf IN abc.gff FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI kim1.out FZ = 4629 FP /^ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP\.\n/ FI outseq FC = 0 FI abc.gff FC = 0 FI x13776.nulloutfile FC = 0 // ID complex-check AQ complex TI 300 CL -omnia IN tembl:x* IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI complex.ujtable FZ = 0 FI x59796.complex FZ = 1438 FP /^ +5 +X07523 +1658 +0\.7314 +\n/ FI x59796.fasta FZ = 21112 FP 12 /^>/ // ID corbatest-check AQ corbatest CC No documentation, no example CL x13776 test.out FI stderr FC < 2 FP 1 /^CORBA support has not been compiled\n/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID entrails-check AQ entrails CL -full IN FI outfile.entrails FZ > 26000 FP /^ +taglist +string +"" +"Extra tags to report"\n/ FP /^ +ausashow +boolean +"N" +"Show the full USA in the alignment"\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID histogramtest-check AQ histogramtest CL -graph ps IN IN IN FI histogramtest.ps FZ > 0 FP /^%%/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created histogramtest.ps\n/ // # this test needs to be kept so stdin can be used for the # valgrind test ID intconv-check AQ intconv CL stdin stdout -auto DL keep IN int main (int argc, char* argv[]) { IN int number; IN long time; IN ajint long[52]; IN ajlong int; IN exit (1); IN } FI stdout FP 4 /ajint/ FP 2 /ajlong/ FZ = 107 // ID patmattest-check AQ patmattest CC No documentation, no example IN tembl:x13776 IN ACA IN FI stdout FC = 93 FP /^ACA\n15 matches found\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID prima-check AQ prima CL -minplen 200 -maxplen 250 IN tembl:v00294 IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI v00294.prima FZ = 1259 FP /^2 pairs found\n/ FP / +266 TTGTCGCGGCGATTAAATCTC +286\s+510 GTACCGTCTTCATGGGAGAAA +530\n/ FP / +452 CTAATGTTCCGGCGTTATTT +471\s+696 TTTGTTGAAAACCGGACATG +715\n/ // ID primers-check RQ primer3 AQ primers CC No documentation, no example IN tembl:k00650 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI k00650.primers FZ = 911 FP /\A\n# PRIMER3 RESULTS FOR K00650\n/ FP /^ 1 PRODUCT SIZE: 264\n/ FP /^ FORWARD PRIMER 2492 20 60\.01 45\.00 AGAATCCGAAGGGAAAGGAA\n/ FP /^ REVERSE PRIMER 2755 20 59\.98 55\.00 CTTCTCCTTCAGCAGGTTGG\n/ // ID seqinfo-check AQ seqinfo CC No documentation, no example IN tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FZ = 163 FP /^Length:[ \t]+2167 basepairs\n/ FP /^GC Content:[ \t]+66\.5436 %\n/ // ID seqretall-check AQ seqretall IN @../../data/eclac.list IN FI j01636.fasta FZ = 15619 FP 5 /^>/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID seqretallfeat-check AQ seqretallfeat CL -osf embl IN @../../data/eclac.list IN x51872ll.embl FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x51872ll.embl FZ = 58672 FP 3 /^ID V00/ FP 5 /^ID / // ID seqretset-check AQ seqretset IN @../../data/eclac.list IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.fasta FZ = 15619 FP 5 /^>/ // ID seqretsingle-check AQ seqretsingle IN @../../data/eclac.list IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI j01636.fasta FZ = 7679 FP 1 /^>/ // ID testplot-check AQ testplot CC No documentation, no example CL -graph ps IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created testplot\.ps\n/ FI testplot.ps FC = 475 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID treetypedisplay-check AQ treetypedisplay CC No documentation, no example CL -graph ps FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created treetypedisplay\.ps\n/ FI treetypedisplay.ps FC = 290 FP /^%%Title: PLplot Graph\n/ FP /^%%Pages: 1\n/ // ID acd-calc-feat AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcfeat ../../data/feat.emft IN IN IN IN IN IN IN FI stderr FC = 2 FP 7 /:/ FP 1 /FLength \[32987\]: / FP 1 /FName: / FP 1 /FBegin \[1\]: / FP 1 /FEnd \[32987\]: / FP 1 /FProtein \[N\]:/ FP 1 /FNucleic \[Y\]: / FP 1 /FSize \[62\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-regexp AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcregexp "abc[def] ghi" IN FI stderr FC = 2 FP 1 /:/ FP 1 /Length \[12\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-seq AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcseq tembl:x13776 IN IN IN IN IN IN FI stderr FC = 2 FP 6 /:/ FP 1 /Length \[2167\]: / FP 1 /Name \[X13776\]: / FP 1 /Begin \[1\]: / FP 1 /End \[2167\]: / FP 1 /Protein \[N\]:/ FP 1 /Nucleic \[Y\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-seqall AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcseqall @../../data/eclac.list IN IN IN IN IN IN FI stderr FC = 2 FP 6 /:/ FP 1 /Length \[7477\]: / FP 1 /Name \[J01636\]: / FP 1 /Begin \[1\]: / FP 1 /End \[7477\]: / FP 1 /Protein \[N\]:/ FP 1 /Nucleic \[Y\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-seqset AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcseqset @../../data/eclac.list IN IN IN IN IN IN IN IN FI stderr FC = 2 FP 8 /:/ FP 1 /Length \[7477\]: / FP 1 /Name \[J01636\]: / FP 1 /Begin \[1\]: / FP 1 /End \[7477\]: / FP 1 /Protein \[N\]:/ FP 1 /Nucleic \[Y\]: / FP 1 /Totweight \[5\.000\]: / FP 1 /Count \[5\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID acd-calc-string AP acdc PP EMBOSS_ACDROOT=../../acd PP export EMBOSS_ACDROOT CL qatestcalcstring "abc def" IN FI stderr FC = 2 FP 1 /:/ FP 1 /Length \[7\]: / FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ######################################################### # # EMBASSY (STRUCTURE) + scopparse (DOMAINATRIX) # ######################################################### ID pdbparse-keep AB structure DL keep TI 120 AA pdbparse IN ../../data/structure IN IN Y IN IN IN FI stdout FC = 3 FP 3 /^Processing / FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI pdbparse.log FC = 18 FP 2 /^SEQRESLENDIF/ FP 2 /^SECSTART 1 1 ILE 384\n/ FP 3 /^SECBOTH/ FP /^SECBOTH 1 1 VAL 78 ILE 81\n/ FI 1cs4.ccf FC = 537 FZ = 51361 FP 475 /^AT / FI 1ii7.ccf FC = 462 FZ = 44223 FP 402 /^AT / FI 2hhb.ccf FC = 5398 FZ = 533177 FP 4779 /^AT / // ID pdbparse-keep2 AB structure DL keep TI 120 AA pdbparse IN ../../data/structure/pdb IN IN Y IN IN IN FI stdout FC = 3 FP 3 /^Processing / FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI pdbparse.log FC = 18 FP 1 /^DUPATOMRES/ FP 5 /^BADINDEX/ FI 1fx2.ccf FC = 2399 FZ = 235429 FP 2141 /^AT / FI 4at1.ccf FC = 8134 FZ = 808419 FP 7170 /^AT / FI 1cs4.ccf FC = 6610 FZ = 654104 FP 5843 /^AT / // ID pdbplus-keep AB structure DL keep AA pdbplus RQ stride RQ naccess CC Requires stride CC Requires naccess IN ../pdbparse-keep/ IN ../../data/structure/ IN IN 3 IN 4 IN IN IN IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP 3 /\S+naccess \S+\.ent/ FP 2 /failures: 0\n/ FI pdbplus.log FC = 28 FP 3 /stride output for/ FP 2 /failures: 0\n/ FI stride.log FC = 0 FZ = 0 FI naccess.log FC = 6 ## ## Yes, naccess does have a typo 'defual' in the message ... ## FP 3 /naccess: using defualt vdw\.radii\n/ FP 3 /naccess: using default STD FILE\n/ FI 1cs4.ccf FC = 537 FZ = 51361 FP /^SQ SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64;\n/ FI 1ii7.ccf FC = 462 FZ = 44223 FP /^SQ SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;\n/ FI 2hhb.ccf FC = 5398 FZ = 533177 FP /^SQ SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64;\n/ // ID scopparse-keep AB domainatrix DL keep AA scopparse IN ../../data/structure/scop.cla.raw IN ../../data/structure/scop.des.raw IN Y IN N IN all.scop FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI all.scop FC = 52 FZ = 809 FP 2 /^ID / // ID domainer-keep AB structure DL keep AA domainer IN ../scopparse-keep/all.scop IN ../pdbplus-keep/ IN IN IN 1 IN domainer_embl.log IN domainer_pdb.log FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^D1CS4A_\n/ FP /^D1II7A_\n/ FI domainer_embl.log FZ = 0 FI domainer_pdb.log FZ = 0 FI d1cs4a_.ent FZ = 29889 FC = 369 FP /^ATOM\s+31\s+CA\s+PHE\s+A\s\d+\s+60\.914 -11\.143 59\.200 1\.00 58\.07\s+C\s+\n/ FI d1cs4a_.ccf FZ = 40517 FC = 418 FP /SQ SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64;\n/ FI d1ii7a_.ent FZ = 29727 FC = 367 FP /ATOM 1 N ASP A 8 7\.977 32\.254 19\.055 1\.00 26\.65 N / FI d1ii7a_.ccf FZ = 39756 FC = 413 FP /SQ SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;/ // ID domainer-keep2 AB structure DL keep AA domainer IN ../../data/structure/all.scop2 IN ../pdbparse-keep2 IN IN IN 1 IN domainer_embl.log IN domainer_pdb.log FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP /^D1CS4A_\n/ FP /^D1FX2A_\n/ FP /^D4AT1B1\n/ FP /^D4AT1D1\n/ FI domainer_embl.log FZ = 0 FI domainer_pdb.log FZ = 0 FI d1cs4a_.ent FZ = 123201 FC = 1521 FP 1476 /ATOM/ FI d1cs4a_.ccf FZ = 166810 FC = 1684 FP /SQ SEQUENCE 225 AA; 25485 MW; F04351B12FCADEE0 CRC64;\n/ FI d1fx2a_.ent FZ = 152928 FC = 1888 FP 1856 /ATOM/ FI d1fx2a_.ccf FZ = 209175 FC = 2110 FP 235 /RE / FI d4at1b1.ent FZ = 60183 FC = 743 FP 725 /ATOM/ FI d4at1b1.ccf FZ = 82089 FC = 835 FP 93 /RE / FI d4at1d1.ent FZ = 60183 FC = 743 FP 725 /ATOM/ FI d4at1d1.ccf FZ = 82089 FC = 835 FP 93 /RE / // ID contacts-keep AB structure DL keep AA contacts IN ../pdbplus-keep/ IN IN 1 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1ii7\n/ FP /^1cs4\n/ FP /^2hhb\n/ FI 1cs4.con FC = 183 FZ = 3744 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .\n/ FP /NC SM 163; LI .\n/ FP /SM ASP 46 ; CYS 47\n/ FI 1ii7.con FC = 172 FZ = 3553 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 .\n/ FP /NC SM 151; LI .\n/ FP /SM ASP 49 ; LEU 50\n/ FI 2hhb.con FC = 2696 FZ = 58358 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 141; NRES2 .\n/ FP /NC SM 643; LI .\n/ FP /SM VAL 1 ; LEU 2\n/ FI contacts.log FC = 3 FZ = 15 FP /1cs4\n/ FP /1ii7\n/ FP /2hhb\n/ // ID contacts-keep2 AB structure DL keep AA contacts IN ../domainer-keep/ IN IN 1 IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^D1II7A_\n/ FP /^D1CS4A_\n/ FI d1cs4a_.con FC = 183 FZ = 3750 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .\n/ FP /NC SM 163; LI .\n/ FP /SM ASP 2 ; ILE 3\n/ FI d1ii7a_.con FC = 172 FZ = 3559 FP /CN MO 1; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 .\n/ FP /NC SM 151; LI .\n/ FP /SM ASP 49 ; LEU 50\n/ FI contacts.log FC = 2 FZ = 16 FP /D1II7A_\n/ FP /D1CS4A_\n/ // ID interface-ex AB structure AA interface IN ../pdbplus-keep/2hhb.ccf IN 1 IN 2hhb.con IN FI stdout FC = 1 FP /^2hhb\n/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI 2hhb.con FC = 274 FZ = 7096 FP /CN MO 1; CN1 1; CN2 2; ID1 A; ID2 B; NRES1 141; NRES2 146\n/ FP 152 /^SM / FI interface.log FC = 1 FP /^2hhb\n/ // ID sites-keep AB structure DL keep TI 120 AA sites IN ../pdbplus-keep IN ../domainer-keep IN ../scopparse-keep/all.scop IN 1 IN IN FI stdout FC = 5 FP /^Entries in HetDic 4306\n/ FP /^Entries in Dbase 4306\n/ FP /CCF FILE:.*/1cs4\.ccf \([1-3]\/3\)/ FP /CCF FILE:.*/1ii7\.ccf \([1-3]\/3\)/ FP /CCF FILE:.*/2hhb\.ccf \([1-3]\/3\)/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI SITES.con FC = 299 FZ = 5261 FP 11 /^ID / FP 3 /^LI ASP 2/ FP /ID PDB 1cs4; DOM d1cs4a_; LIG POP;\n/ FI sites.log FC = 3 FP /^CCF:.*1cs4\.ccf HETS:YES NHETS:7 SCOP:YES NDOMS: 1\n/ FP /^CCF:.*1ii7\.ccf HETS:YES NHETS:5 SCOP:YES NDOMS: 1\n/ FP /^CCF:.*2hhb\.ccf HETS:YES NHETS:5 SCOP:NO NCHN:4\n/ // ID hetparse-ex AB structure AA hetparse IN ../../data/structure/het.txt IN Y IN IN Ehet.dat FP 2 /^Processing/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI Ehet.dat FC = 48 FZ = 949 FP 9 /^NN/ // ID pdbtosp-keep AB structure DL keep AA pdbtosp IN ../../data/structure/pdbtosp.txt IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI Epdbtosp.dat FC = 49 FZ = 422 FP 7 /^EN / FP /^IN XYLA_ACTMI ID; P12851 ACC;\n/ // ######################################################### # # EMBASSY (DOMAINATRIX) # ######################################################### ID cathparse-ex AB domainatrix AA cathparse IN ../../data/structure/caths.list.small IN ../../data/structure/domlist.small IN ../../data/structure/CAT.names.all.small IN IN FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI Ecath.dat FC = 48 FZ = 606 FP 2 /^ID/ FP /CH 0 CHAIN; 156 START; 203 END;\n/ FP /CH 0 CHAIN; 159 START; 202 END;\n/ FP /NR 48\n/ FP /NR 44\n/ FP 2 /SF DNA helicase RuvA subunit, C-terminal domain\n/ FI cathparse.log FC = 8 FZ = 64 FP 4 /^1\.10\.8/ // ID domainseqs-keep AB domainatrix DL keep AA domainseqs IN ../scopparse-keep/all.scop IN ../domainer-keep IN Y IN ../pdbtosp-keep/Epdbtosp.dat IN all_s.scop IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FZ = 38 FP 2 /^\/\/\n/ FI all_s.scop FC = 59 FZ = 1080 FP 2 /^ID / FI domainseqs.log FC = 6 FZ = 78 FP 2 /^NO_ACCESSION_NUMBER\n/ FP 2 /\/\/\n/ FP /^D1CS4A_ +\n/ FP /^D1II7A_ +\n/ // ID domainnr-ex AB domainatrix AA domainnr IN ../domainseqs-keep/all_s.scop IN IN 1 IN 1 IN 5 IN all_nr.scop IN FI stdout FC = 3 FP 1 /^\/\/ / FP 2 /^D1/ FI stderr FC = 15 FP 0 /Error: / FP 0 /Died: / FI all_nr.scop FC = 30 FZ = 535 FP 1 /^ID/ FI domainnr.log FC = 7 FZ = 117 FP 1 /^Retained/ FP 1 /^Rejected/ FP 1 /^\/\/ / // ID domainreso-ex AB domainatrix AA domainreso IN ../domainer-keep/ IN ../scopparse-keep/all.scop IN 2.3 IN all_2.3.scop FI stdout FC = 2 FP 2 /\.ccf\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI all_2.3.scop FC = 26 FZ = 390 FP 1 /^ID/ FP /SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;\n/ // ID domainsse-keep AB domainatrix DL keep AA domainsse IN ../scopparse-keep/all.scop IN ../domainer-keep IN domainsse.out IN domainsse.log FI stdout FC = 6 FP 2 /^Processing/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI domainsse.out FC = 62 FZ = 1068 FP 2 /^ID / FI domainsse.log FZ = 0 // ID ssematch-ex AB domainatrix AA ssematch IN ../../data/structure/sse.in IN ../domainsse-keep/domainsse.out IN 1 IN res.dcf IN elm.dcf IN FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI res.dcf FC = 33 FZ = 551 FP 1 /^ID / FI elm.dcf FC = 33 FZ = 581 FP 1 /^ID / FP /^SE HH\n/ FI ssematch.log FC = 0 FZ = 0 // ######################################################### # # EMBASSY (DOMALIGN) + seqsearch (DOMSEARCH) # ######################################################### ID domainrep-keep AB domalign DL keep AA domainrep RQ stamp CC requires a modified stamp to be installed IN ../../data/structure/all.scop2 IN 2 IN all_rep1st.scop FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 6 FP 6 /stamp/ FI all_rep1st.scop FC = 104 FZ = 1785 FP 4 /^ID/ // ID domainalign-keep AB domalign DL keep AA domainalign PP mkdir daf RQ stamp CC requires a modified stamp to be installed IN ../../data/structure/all.scop2 IN IN 4 IN 1 IN N IN daf IN IN FI stderr FC = 15 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 108 FP 4 /^\S+\/stamp/ FI 54894.ent FC = 1461 FZ = 117967 FP 11 /^REMARK/ DI daf DF 54894.daf DF 55074.daf ## FI daf/54894.daf ## FC = 21 ## FZ = 856 ## FP 6 /^# XX/ FI 55074.ent FC = 3343 FZ = 270409 FP 11 /^REMARK/ ## FI daf/55074.daf ## FC = 36 ## FZ = 1773 ## FP 6 /^# XX/ FI domainalign.log FC = 14 FZ = 574 FP 14 /^Replaced/ // ID allversusall-ex AB domalign AA allversusall IN ../../data/structure/allversusall/ IN IN FI stdout FC = 2 FP /swtiny1\.fasta\n/ FP /swtiny2\.fasta\n/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI swtiny1.out FC = 10 FZ = 280 FP /1 Q9WVI4 : 2 Q9ERL9 : 90\.48\n/ FP /2 Q9ERL9 : 3 Q9DGG6 : 58\.28\n/ FP /3 Q9DGG6 : 4 Q99396 : 52\.26\n/ FP /4 Q99396 : 5 Q99280 : 83\.41\n/ FI swtiny2.out FC = 3 FZ = 84 FP /1 O58452 : 2 O30129 : 82\.42\n/ FP /1 O58452 : 3 O26938 : 75\.56\n/ FP /2 O30129 : 3 O26938 : 71\.43\n/ FI allversusall.log FC = 4 FP 2 /^\/\/\n/ FP /swtiny1\.fasta\n/ FP /swtiny2\.fasta\n/ // ######################################################### # # EMBASSY (DOMSEARCH) + seqalign (DOMALIGN) # ######################################################### ID seqsearch-keep RQ blastpgp ## Uses blastpgp to search ## blastpgp generates 4 warning messages ## (WARNING so the test pattern misses it) in stderr AB domsearch DL keep AA seqsearch IN 2 IN ../domainalign-keep/daf IN ../../data/structure/swsmall IN IN 0.0001 IN 100 IN IN FI stderr FC = 12 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP 2 /^\S+blastpgp/ FI 54894.dhf FC = 80 FZ = 13751 FP 40 /^>/ FI 55074.dhf FC = 200 FZ = 37208 FP 100 /^>/ FI seqsearch.log FC = 4 FP 2 /\.daf\n/ FP 2 /^\/\/\n/ // ID seqfraggle-keep AB domsearch DL keep AA seqfraggle IN ../seqsearch-keep IN 50 IN FI stdout FC = 2 FP /Processing .*54894\.dhf\n/ FP /Processing .*55074\.dhf\n/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI 54894.dhf FZ = 13471 FC = 80 FP 40 /^>/ FI 55074.dhf FZ = 34703 FC = 186 FP 93 /^>/ // ID seqnr-keep AB domsearch DL keep AA seqnr PP mkdir hitsnr PP mkdir hitsred IN ../seqfraggle-keep IN N IN Y IN ../domainalign-keep/daf IN 1 IN 70 IN hitsnr IN Y IN hitsred IN FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP 2 /^Processing/ FI seqnr.log FC = 4 FP 2 /^\/\/\n/ FP 2 /\.dhf\n/ DI hitsnr DF 54894.dhf DF 55074.dhf ## FI hitsnr/54894.dhf ## FZ = 1351 ## FC = 8 ## FP 4 /^>/ ## hitsnr/55074.dhf ## FZ = 2512 ## FC = 14 ## FP 7 /^>/ DI hitsred DF 54894.dhf DF 55074.dhf ## FI hitsred/54894.dhf ## FZ = 12120 ## FC = 72 ## FP 36 /^>/ ## FI hitsred/55074.dhf ## FZ = 32611 ## FC = 174 ## FP 87 /^>/ // ID seqsort-keep AB domsearch DL keep AA seqsort IN ../seqnr-keep/hitsnr IN 10 IN Y IN Y IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI fam.dhf FC = 22 FZ = 3863 FP 11 /^> / FI oth.dhf FC = 0 FZ = 0 FI 54894.dhf FC = 8 FZ = 1351 FP 4 /^> / FI 55074.dhf FC = 14 FZ = 2512 FP 7 /^> / // ID seqwords-ex AB domsearch AA seqwords IN ../../data/structure/seqwords.terms IN ../../data/structure/seqwords.seq IN seqwords.dhf FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI seqwords.dhf FC = 2 FZ = 531 FP /^> Q60150\^.\^1\^312\^SCOP\^.\^0\^Alpha and beta proteins/ // ID seqalign-keep AB domalign AA seqalign DL keep TI 300 RQ clustalw ## Apparently requires clustalw 1.83 for long filenames ## clustalw 1.82 failed with 'unable to read .aln file' ## this was a clustalw error message ## renaming the files and running clustalw worked IN 2 IN ../domainalign-keep/daf IN ../seqsearch-keep IN 1 IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 6344 FP 144 /Sequence \d+: .* \d+ aa\n/ FI 54894.daf FC = 98 FZ = 6987 FP 2 /d4at1b1_0/ FP 2 /d4at1d1_1/ FI 55074.daf FC = 527 FZ = 42762 FP 5 /d1cs4a__0/ FP 5 /d1fx2a__1/ FI seqalign.log FC = 4 FP 2 /\.daf\n/ FP 2 /^\/\/\n/ // ######################################################### # # EMBASSY (SIGNATURE) # ######################################################### ID siggen-keep AB signature DL keep AA siggen IN ../domainalign-keep/daf IN 2 IN 5 IN 1 IN EBLOSUM62 IN 15 IN 0 IN Y IN CC output filename not set FI stderr FC = 16 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 54894.sig FC = 136 FZ = 1367 FP 15 /^IN / FI 55074.sig FC = 364 FZ = 3520 FP 38 /^IN / // ID siggenlig-keep AB signature DL keep AA siggenlig IN ../sites-keep/SITES.con IN ../pdbplus-keep IN ../domainer-keep IN 1 IN 1 IN IN FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FZ = 0 FI 101.1.F.#.1cs4.d1cs4a_.sig FC = 62 FZ = 610 FP /^IN / FI 101.2.F.#.1ii7.d1ii7a_.sig FC = 30 FZ = 318 FP /^IN / FI FOK.1.F.#.1cs4.d1cs4a_.sig FC = 22 FZ = 219 FP /^IN / FI HEM.1.F.#.2hhb...sig FC = 150 FZ = 1415 FP /^IN / FI HEM.2.F.#.2hhb...sig FC = 150 FZ = 1415 FP /^IN / FI HEM.3.F.#.2hhb...sig FC = 166 FZ = 1563 FP /^IN / FI HEM.4.F.#.2hhb...sig FC = 134 FZ = 1267 FP /^IN / FI MG.1.F.#.1cs4.d1cs4a_.sig FC = 46 FZ = 441 FP /^IN / FI MN.1.F.#.1ii7.d1ii7a_.sig FC = 38 FZ = 373 FP /^IN / FI PO4.1.F.#.2hhb...sig FC = 30 FZ = 290 FP /^IN / FI POP.1.F.#.1cs4.d1cs4a_.sig FC = 62 FZ = 590 FP /^IN / FI siggenlig.log FC = 0 FZ = 0 // ID libgen-ex AB signature AA libgen RQ hmmer RQ sam-t2k IN ../domainalign-keep/daf IN EBLOSUM62 IN 2 IN FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 54894.disc FC = 107 FZ = 14558 FP /Length\s+94\n/ FI 55074.disc FC = 265 FZ = 38268 FP /Length\s+252\n/ // ID matgen3d-ex AB signature AA matgen3d IN 1 IN ../scopparse-keep/all.scop IN ../domainer-keep IN 1 IN IN IN FI stderr FC = 22 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI stdout FC = 0 FZ = 0 FI matgen3d.calc FC = 128 FZ = 3801 FP /SUMiNijArr/ FI matgen3d.log FC = 182 FZ = 2686 FP 1 /D1CS4A/ FP 1 /D1II7A_/ FI matgen3d.out FC = 28 FZ = 3563 FP 1 /AU -0\.01 1\.19 0\.91 0\.50 1\.19 0\.68 -0\.11 2\.00 1\.19 0\.35 -0\.11 0\.91 2\.29 0\.35 2\.29 1\.60 1\.19 -2\.20 2\.29 1\.19 -2\.20 -2\.20 -2\.20 -2\.64/ // ID sigscan-ex AB signature AA sigscan IN ../siggen-keep/54894.sig IN ../../data/structure/swsmall IN IN IN IN IN IN IN CC depends on siggen-keep test FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 5 / ok\n/ FI SIGSCAN.dhf FC = 200 FP /> P00478/ FI SIGSCAN.aln FC = 1113 FZ = 73700 FP /^SIGNATURE - ----------\*-\*--------------------------\*-------------\n/ // ID sigscanlig-ex AB signature AA sigscanlig PP mkdir lhf PP mkdir aln PP mkdir results IN ../siggenlig-keep IN ../../data/structure/swtiny IN IN 1 IN IN IN IN lhf IN aln IN results FI stderr FC = 9 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 DI lhf DF Q99396^.^262^473^.^55074^Alpha.lhf DF Q9DGG6^.^380^560^.^55074^Alpha.lhf DF Q9ERL9^.^480^631^.^55074^Alpha.lhf DF Q9WVI4^.^516^664^.^55074^Alpha.lhf DI aln DF Q99396^.^262^473^.^55074^Alpha.aln DF Q9DGG6^.^380^560^.^55074^Alpha.aln DF Q9ERL9^.^480^631^.^55074^Alpha.aln DF Q9WVI4^.^516^664^.^55074^Alpha.aln DI results DF Q99396^.^262^473^.^55074^Alpha.results DF Q9DGG6^.^380^560^.^55074^Alpha.results DF Q9ERL9^.^480^631^.^55074^Alpha.results DF Q9WVI4^.^516^664^.^55074^Alpha.results // ID rocon-ex AB signature AA rocon IN ../../data/structure/rocon/rocon.dhf IN ../../data/structure/rocon.valid IN 10 IN 1 IN rocon.hits FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rocon.hits FC = 9 FZ = 308 FP 3 /^TRUE / FP 2 /^FALSE / FP 2 /^CROSS / FP 1 /^UNKNOWN / // ID rocplot-ex AB signature AA rocplot IN ../../data/structure/rocplot/hitsin IN 2 IN 2 IN 1 IN IN IN IN IN FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^Processing / FI _rocplot FC = 12 FZ = 353 FP /^plot "_rocplot_dat0" smooth bezier title "Combined dataset \(0\.185\)"\n/ FI _rocplot_dat0 FC = 81 FZ = 1242 FP /^0\.625 0\.214\n/ FI _classplot FC = 9 FZ = 580 FP /^plot "_classplot_dat0" .* "_classplot_dat4" .* title "False hits"\n/ FI _classplot_dat0 FC = 81 FZ = 1315 FP /^80\.000 0\.375\n/ FI _classplot_dat1 FC = 81 FZ = 1316 FP /^80\.000 0\.100\n/ FI _classplot_dat2 FC = 81 FZ = 1320 FP /^80\.000 0\.050\n/ FI _classplot_dat3 FC = 81 FZ = 1318 FP /^80\.000 0\.100\n/ FI _classplot_dat4 FC = 81 FZ = 1316 FP /^80\.000 0\.375\n/ FI _summary FC = 11 FZ = 333 FP /ROC50 == 0\.185 \(combined\)/ FI rocplot.log FC = 33 FP /^rocn\[0\]:/ FP /^numfiles: 2\n/ // ###################################### # EMNU ####################################### ID emnu-ex AB emnu AA emnu CL -explode IK  IK IK y FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FK stdout FC > 3 FP /^emnu version: 1\.05\n/ FP /^EMBOSS Simple Menu\n/ FP /ALPHABETIC LISTING OF ALL PROGRAMS/ FP /ALIGNMENT GLOBAL/ // ####################################### # ESIM4 ####################################### ID esim4-ex AB esim4 AA esim4 ## Test example copied from est2genome ## Similar results - possible longer alignment at 3' end of EST. IN tembl:h45989 IN tembl:z69719 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI h45989.esim4 FC = 7 FP /^seq1 = H45989, 495 bp\n/ FP /^seq2 = Z69719 \(Z69719\), 33760 bp\n/ FP /^1-193 \(25686-25874\) 92% <-\n/ FP /^194-407 \(26279-26492\) 98% <-\n/ FP /^408-487 \(27391-27469\) 88%\n/ // #################################################### # HMMERNEW # 1. Examples taken mostly from hmmer 2.3.2 tutorial # 2. Data lives in: /emboss/emboss/test/data/hmmnew # 3. Do not use FZ lines as hmmer tends to write # date info. to output files. #################################################### ID ehmmbuild-ex-keep AB hmmernew RQ hmmer AA ehmmbuild DL keep CL ../../data/hmmnew/globins50.msf globin.hmm -nhmm globins50 -strategy D FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Build a profile HMM from an alignment\.\n/ FI stdout FC = 37 FP /^\S+hmmbuild -n globins50 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F globin\.hmm \.\.\/\.\.\/data\/hmmnew\/globins50\.msf\n/ FP /^Average score: 189\.04 bits\n/ FP /^Constructed a profile HMM \(length 143\)\n/ FI globin.hmm FC = 447 FP /^COM \S+hmmbuild -n globins50 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F globin\.hmm \.\.\/\.\.\/data\/hmmnew\/globins50\.msf\n/ FP /^CKSUM 9858\n/ // ID ehmmbuild-ex2-keep AB hmmernew RQ hmmer AA ehmmbuild DL keep CL ../../data/hmmnew/rrm.sto myhmms -nhmm rrm -strategy D FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Build a profile HMM from an alignment\.\n/ FI stdout FC = 37 FP /^\S+hmmbuild -n rrm --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/rrm\.sto\n/ FP /^Constructed a profile HMM \(length 77\)\n/ FI myhmms FC = 249 FP /^COM \S+hmmbuild -n rrm --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/rrm\.sto\n/ FP /^CKSUM 8325\n/ // ID ehmmbuild-ex3-keep AB hmmernew RQ hmmer AA ehmmbuild DL keep ## myhmms is overwritten, so copy file to ensure output of previous test is not overwritten. PP cp ../ehmmbuild-ex2-keep/myhmms ./ CL ../../data/hmmnew/fn3.sto myhmms -nhmm fn3 -strategy D FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Build a profile HMM from an alignment\.\n/ FI stdout FC = 37 FP /^\S+hmmbuild -n fn3 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/fn3\.sto\n/ FP /^Constructed a profile HMM \(length 84\)\n/ FI myhmms FC = 523 FP /^COM \S+hmmbuild -n rrm --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/rrm\.sto\n/ FP /^COM \S+hmmbuild -n fn3 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/fn3\.sto\n/ FP /^CKSUM 8325\n/ FP /^CKSUM 6130\n/ // ID ehmmbuild-ex4-keep AB hmmernew RQ hmmer AA ehmmbuild DL keep ## myhmms is overwritten, so copy file to ensure output of previous test is not overwritten. PP cp ../ehmmbuild-ex3-keep/myhmms ./ CL ../../data/hmmnew/pkinase.sto myhmms -nhmm pkinase -strategy D FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Build a profile HMM from an alignment\.\n/ FI stdout FC = 37 FP /^\S+hmmbuild -n pkinase --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/pkinase\.sto\n/ FP /^Constructed a profile HMM \(length 294\)\n/ FI myhmms FC = 1427 FP /^COM \S+hmmbuild -n rrm --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/rrm\.sto\n/ FP /^COM \S+hmmbuild -n fn3 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/fn3\.sto\n/ FP /^COM \S+hmmbuild -n pkinase --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/pkinase\.sto\n/ FP /^CKSUM 8325\n/ FP /^CKSUM 6130\n/ FP /^CKSUM 4536\n/ // ID ehmmcalibrate-ex-keep AB hmmernew RQ hmmer AA ehmmcalibrate TI 120 DL keep CL ../ehmmbuild-ex-keep/globin.hmm globino.hmm -seed 1 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Calibrate HMM search statistics\n/ FI stdout FC = 21 FP /^\S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex-keep\/globin\.hmm\n/ FP /^HMM file: \.\.\/ehmmbuild-ex-keep\/globin\.hmm\n/ FI globino.hmm FC = 449 FP /^COM \S+hmmbuild -n globins50 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F globin\.hmm \.\.\/\.\.\/data\/hmmnew\/globins50\.msf\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex-keep\/globin\.hmm\n/ FP /^CKSUM 9858\n/ // ID ehmmcalibrate-ex2-keep AB hmmernew RQ hmmer AA ehmmcalibrate DL keep TI 120 CL ../ehmmbuild-ex4-keep/myhmms myhmmso -seed 1 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /Calibrate HMM search statistics\n/ FI stdout FC = 31 FP /^\S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^HMM file: \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FI myhmmso FC = 1433 FP /^COM \S+hmmbuild -n rrm --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/rrm\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^COM \S+hmmbuild -n fn3 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/fn3\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^COM \S+hmmbuild -n pkinase --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/pkinase\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^CKSUM 8325\n/ FP /^CKSUM 6130\n/ FP /^CKSUM 4536\n/ // ID ehmmsearch-ex-keep AB hmmernew RQ hmmer AA ehmmsearch DL keep CL ../ehmmcalibrate-ex-keep/globino.hmm ../../data/hmmnew/Artemia.fa globino.ehmmsearch -a 100 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Search a sequence database with a profile HMM\n/ FI stdout FC = 3 FP /^\S+hmmsearch -A 100 -E 10\.000000 -T -1000000\.000000 -Z 0 --domE 1000000\.000000 --domT -1000000\.000000 \.\.\/ehmmcalibrate-ex-keep\/globino\.hmm \.\.\/\.\.\/data\/hmmnew\/Artemia\.fa > globino\.ehmmsearch\n/ FI globino.ehmmsearch FC = 216 FP /^HMM file: \.\.\/ehmmcalibrate-ex-keep\/globino\.hmm \[globins50\]\n/ FP /^ Total hits: 1\n/ FP /^ Total hits: 9\n/ // ID ehmmpfam-ex-keep AB hmmernew RQ hmmer AA ehmmpfam DL keep CL ../ehmmcalibrate-ex2-keep/myhmmso ../../data/hmmnew/7LES_DROME myhmmso.ehmmpfam -A 10 -E 10 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Search one or more sequences against an HMM database\.\n/ FI stdout FC = 3 ## This is not the full command-line so as to avoid checking against a (variable) temp. file name. FP /^\S+hmmpfam -A 10 -E 10\.000000 -T -1000000\.000000 -Z 59021 --domE 1000000\.000000 --domT -1000000\.000000 --informat FASTA \.\.\/ehmmcalibrate-ex2-keep\/myhmmso/ FI myhmmso.ehmmpfam FC = 137 FP /^HMM file: \.\.\/ehmmcalibrate-ex2-keep\/myhmmso\n/ FP /^fn3 6/6/ FP /^pkinase 1/1/ // ID ehmmalign-ex-keep AB hmmernew RQ hmmer AA ehmmalign DL keep CL ../ehmmcalibrate-ex-keep/globino.hmm ../../data/hmmnew/globins630.fa globins630.ali FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP /^Align sequences to an HMM profile\n/ FP 0 /Died: / FI stdout FC = 13 ## This is not the full command-line so as to avoid checking against a (variable) temp. file name. FP /^\S+hmmalign --informat FASTA --outformat A2M -o globins630\.ali \.\.\/ehmmcalibrate-ex-keep\/globino\.hmm/ FP /^Alignment saved in file globins630\.ali\n/ FI globins630.ali FC = 3150 FP /^>BAHG_VITSP \n/ FP /^>MYG_ZIPCA \n/ // ID ehmmconvert-ex-keep AB hmmernew RQ hmmer AA ehmmconvert DL keep CL ../ehmmcalibrate-ex-keep/globino.hmm globino.ehmmconvert -format G FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Convert between profile HMM file formats\n/ FI stdout FC = 16 FP /^\S+hmmconvert -p -F \.\.\/ehmmcalibrate-ex-keep\/globino\.hmm globino\.ehmmconvert\n/ FP /^1 HMM\(s\) converted and written to globino\.ehmmconvert\n/ FI globino.ehmmconvert FC = 169 FP /^\(Peptide\) HMMCONVERT v2\.3\.2 Length: 143 globins50||\n/ FP /^ \* 621 74 359 488 301 325 254 392 570 697 178 318 209 339 312 490 400 555 65 192 0 0 0 0 \n/ // ID ehmmemit-ex-keep AB hmmernew RQ hmmer AA ehmmemit DL keep CL ../ehmmcalibrate-ex-keep/globino.hmm globino.ehmmemit -c N -n 10 FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Generate sequences from a profile HMM\.\n/ FI stdout FC = 14 FP /^\S+hmmemit --seed 0 -n 10 -o globino\.ehmmemit \.\.\/ehmmcalibrate-ex-keep\/globino\.hmm\n/ FP /^Output saved in file globino\.ehmmemit\n/ FI globino.ehmmemit FC = 40 FP /^>globins50-1 \n/ FP /^>globins50-10 \n/ FP /^AEQAIEMQLWHAVANAKKVEEEQVKRLYQDERGSTAHFMHYEKLRNNNDK\n/ // ID ehmmindex-ex-keep AB hmmernew RQ hmmer AA ehmmindex DL keep ## Outfile will be created in same directory as input file, therefore copy input file first. PP cp ../ehmmcalibrate-ex2-keep/myhmmso ./ CL myhmmso FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Create a binary SSI index for an HMM database\.\n/ FI stdout FC = 18 FP /^\S+hmmindex \.\/myhmmso\n/ FP /^SSI index: \.\/myhmmso\.ssi\n/ FP /^# of HMMS: 3\n/ FI myhmmso.ssi FP /pkinase/ FP /fn3/ FZ = 178 ## Each file, including those copied in, needs a test. ## Use the test for myhmmso from ehmmcalibrate-ex2-keep ## Can't use 'QQ rm myhmmso' as both myhmmso & myhmmso.ssi are needed by the next test. FI myhmmso FC = 1433 FP /^COM \S+hmmbuild -n rrm --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/rrm\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^COM \S+hmmbuild -n fn3 --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/fn3\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^COM \S+hmmbuild -n pkinase --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/pkinase\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^CKSUM 8325\n/ FP /^CKSUM 6130\n/ FP /^CKSUM 4536\n/ // ID ehmmfetch-ex-keep AB hmmernew RQ hmmer AA ehmmfetch DL keep CL ../ehmmindex-ex-keep/myhmmso pkinase pkinase.ehmmfetch FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Retrieve an HMM from an HMM database\.\n/ FI stdout FC = 3 FP /^\S+hmmfetch \.\.\/ehmmindex-ex-keep\/myhmmso pkinase > pkinase\.ehmmfetch\n/ FI pkinase.ehmmfetch FC = 906 FP /^COM \S+hmmbuild -n pkinase --pbswitch 1000 --archpri 0\.850000 --idlevel 0\.620000 --swentry 0\.500000 --swexit 0\.500000 --wgsc -A -F myhmms \.\.\/\.\.\/data\/hmmnew\/pkinase\.sto\n/ FP /^COM \S+hmmcalibrate --mean 350\.000000 --num 5000 --sd 350\.000000 --seed 1 \.\.\/ehmmbuild-ex4-keep\/myhmms\n/ FP /^CKSUM 4536\n/ // ####################################### # HMMER # demo directory ../../data/hmm # has example files from the hmmer 2.1.1 tutorial ####################################### ID ohmmbuild-ex-keep AB hmmer AA ohmmbuild DL keep CL ../../data/hmm/globins50.msf globin.hmm -auto FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Maximum score: 340\.28 bits\n/ FI globin.hmm FC = 461 FP /^HMMER2\.0\n/ FP /^CKSUM 8939\n/ FI globins50.out2 FC = 260 FP /^#=SQ HBB2_TRICR 0\.5211 HBB2_TRICR - 0\.\.0\:\:0 -\n/ FI globins50.out3 FC = 439 FP /^M 0\.00 0\.00 0\.00 0\.00 0\.00 0\.77 0\.00 .* 6\.77 0\.62 0\.00 0\.00 0\.00 \n/ // ID ohmmcalibrate-ex-keep AB hmmer AA ohmmcalibrate TI 120 DL keep ## copy the input file because it will be updated ## Provide a seed value to get reproducible output for validation PP cp ../ohmmbuild-ex-keep/globin.hmm ./ CL globin.hmm -seed 1079460101 -auto FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globin.ohmmcalibrate FC = 13 FP /Number of samples: 5000\n/ FI globin.out2 FC = 33 FP /% Statistical details of theoretical EVD fit:\n/ FI globin.hmm FC = 463 FP /^COM ohmmbuild \.\.\/\.\.\/data\/hmm\/globins50\.msf globin\.hmm -auto\n/ FP /^COM ohmmcalibrate globin\.hmm -seed 1079460101 -auto\n/ FP 2 /^COM/ // ID ohmmsearch-ex AB hmmer AA ohmmsearch CL ../../data/hmm/Artemia.fa ../ohmmcalibrate-ex-keep/globin.hmm -auto FI stderr FC = 0 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI s13421.ohmmsearch FC = 60 FP /S13421 1/1 149 284 \.\. 1 138 \[\. 66\.9 3\.3e-16\n/ FP / Total hits: 1\n/ // ID ohmm-own-keep1 AB hmmer AA ohmmbuild DL keep CL ../../data/hmm/rrm.slx -sf selex rrm.hmm FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 70\n/ FI rrm.hmm FC = 236 FP /^LENG 72\n/ FI rrm.out2 FC = 216 FP /^#=SQ CABA_MOUSE\/77-148 0\.9361 CABA_MOUSE\/77-148 - 0\.\.0\:\:0 -\n/ FI rrm.out3 FC = 214 FP /^M 2\.15 0\.89 [0\. ]+ 20\.39 0\.00 31\.19 0\.94 [0\. ]+ 12\.44 [0\. ]+ \n/ // ID ohmm-own-keep2 AB hmmer AA ohmmbuild CL ../../data/hmm/fn3.slx -sf selex fn3.hmm QQ cp fn3.hmm ../ohmm-own-keep1/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 109\n/ FI fn3.hmm FC = 275 FP /^LENG 85\n/ FI fn3.out2 FC = 444 FP /^#=SQ 7LES_DROVI/1917-1997 1\.1765 7LES_DROVI/1917-1997 - 0\.\.0\:\:0 -\n/ FI fn3.out3 FC = 253 FP /^M 5\.00 0\.00 18\.68 3\.14 0\.00 11\.07 0\.00 0\.00 .* 0\.00 1\.18 \n/ // ID ohmm-own-keep3 AB hmmer AA ohmmbuild CL ../../data/hmm/pkinase.slx -sf selex pkinase.hmm QQ cp pkinase.hmm ../ohmm-own-keep1/ FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 67\n/ FI pkinase.hmm FC = 770 FP /^LENG 250\n/ FI pkinase.out2 FC = 759 FP /^#=SQ ABL1_CAEEL/296-547 0\.9227 ABL1_CAEEL/296-547 - 0\.\.0\:\:0 -\n/ FI pkinase.out3 FC = 748 FP /^M 0\.00 1\.05 2\.01 3\.10 5\.95 .* 3\.94 1\.05 3\.97 8\.75 0\.00 0\.93 \n/ // ID ohmm-own-keep4 AB hmmer PP cat ../ohmm-own-keep1/*.hmm > myhmms AA ohmmcalibrate DL keep TI 300 CL myhmms -seed 1079460101 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI myhmms FC = 1287 FP /^LENG 250\n/ FI myhmms.ohmmcalibrate FC = 23 FP /^\n/ FI myhmms.out2 FC = 109 FP /^HMM: 7LES_DROME/2209-2481\n/ FP /^chi-sq statistic = 64\.6846\n/ // ID ohmm-own2-keep1 AB hmmer AA ohmmbuild DL keep CL ../../data/hmm/rrm.sto -sf stockholm myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 90\n/ FI myhmms FC = 236 FP /^LENG 72\n/ FI rrm.out2 FC = 368 FP /^#=SQ CABA_MOUSE\/77-147 0\.8372 CABA_MOUSE\/77-147 - 0\.\.0\:\:0 -\n/ FI rrm.out3 FC = 214 FP /^M 3\.11 1\.98 [0\. ]+ 26\.56 0\.00 35\.41 0\.84 [0\. ]+ 20\.11 [0\. ]+ \n/ // ID ohmm-own2-keep2 AB hmmer AA ohmmbuild CL -append ../../data/hmm/fn3.slx -sf selex ../ohmm-own2-keep1/myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 109\n/ FI fn3.out2 FC = 444 FP /^#=SQ 7LES_DROVI/1917-1997 1\.1765 7LES_DROVI/1917-1997 - 0\.\.0\:\:0 -\n/ FI fn3.out3 FC = 253 FP /^M 5\.00 0\.00 18\.68 3\.14 0\.00 11\.07 0\.00 0\.00 .* 0\.00 1\.18 \n/ // ID ohmm-own2-keep3 AB hmmer AA ohmmbuild CL -append ../../data/hmm/pkinase.slx -sf selex ../ohmm-own2-keep1/myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 31 FP /^Number of sequences: 67\n/ FI pkinase.out2 FC = 759 FP /^#=SQ ABL1_CAEEL/296-547 0\.9227 ABL1_CAEEL/296-547 - 0\.\.0\:\:0 -\n/ FI pkinase.out3 FC = 748 FP /^M 0\.00 1\.05 2\.01 3\.10 5\.95 .* 3\.94 1\.05 3\.97 8\.75 0\.00 0\.93 \n/ // ID ohmm-own2-keep4 AB hmmer AA ohmmcalibrate DL keep TI 300 PP cp ../ohmm-own2-keep1/myhmms . CL myhmms -seed 1079460101 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI myhmms FC = 772 FP /^LENG 250\n/ FI myhmms.ohmmcalibrate FC = 13 FP /^\n/ FI myhmms.out2 FC = 35 FP /^chi-sq statistic = 48\.4214\n/ // ID ohmmpfam-ex AB hmmer AA ohmmpfam CL ../../data/hmm/7LES_DROME ../ohmm-own-keep4/myhmms IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 48 FP /^\n/ FP /^ CS EAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSS \n/ FP /^ RF EAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSS \n/ FP /^ \.\.\.\.\.\.wneltvpgtttsytltgLkPgteYtvrVqAvnggGnGpeS<-\*\n/ FP /^ \+\+\+\+\+ \+ \+\+\+ t\+ \+\+ ltg kPg\+ Y\+\+\+VqA\+ \+ \+ \+ S \n/ FP /^ 7LES_DROME 1846 qdrrewEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSS 1891 \n/ FI 7les_drome.ohmmpfam FC = 18 FP /^7LES_DROME\/1799-1891: domain 1 of 1, from 1799 to 1891: score 62\.6, E = 3\.9e-15\n/ FP /^7LES_DROME\/2209-2481 1\/1 2209 2481 \.\. 1 248 \[\. 303\.5 2\.5e-87\n/ // ID ohmmalign-keep AB hmmer AA ohmmalign DL keep CL ../ohmmbuild-ex-keep/globin.hmm ../../data/hmm/globins630.fa globins630.ali FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Alignment saved in file globins630\.ali\n/ FI globins630.ali FC = 5688 FP /^#=SQ HBB_HUMAN 1\.0000 HBB_HUMAN - 0\.\.0\:\:0 -\n/ FP 3 /^HBB_HUMAN \.+\n/ FP 5 /^HBB_HUMAN \./ FP /^HBB_HUMAN \.\.LKGTFATLSELHCDKL\.\.\.\.HVDPENFRLL\.GNVLVCVLAHHF\.G\.KE\n/ // ID ohmmconvert-ex AB hmmer AA ohmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm\.hmm\n/ FI rrm.hmm FC = 237 FP /^LENG 72\n/ // ID ohmmconvert-exb AB hmmer AA ohmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm -format b FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm\.hmm\n/ FI rrm.hmm FC = 23 FP 4 /rrm/ // ID ohmmconvert-exg AB hmmer AA ohmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm -format g FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm\.hmm\n/ FI rrm.hmm FC = 91 FP /^!!AA_PROFILE 1\.0\n/ FP /^\(Peptide\) HMMCONVERT v2\.1\.1 Length: 72 rrm\|\|\n/ FP /^ F -364 -346 -598 -534 .* -260 110 111\n/ // ID ohmmconvert-exx AB hmmer AA ohmmconvert CL ../../data/hmm/rrm.hmm rrm.hmm -format x FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP /^1 HMM\(s\) converted and written to rrm\.hmm\n/ FI rrm.hmm FP /^!!AA_PROFILE 1\.0\n/ FP /^\(Peptide\) HMMCONVERT v2\.1\.1 Length: 72 rrm\|\|\n/ FP /^ F -364 -346 -598 -534 .* -260 110 111 116 137\n/ // ID ohmmemit-ex AB hmmer AA ohmmemit CL ../../data/hmm/rrm.hmm -seed 1079460101 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI rrm.ohmmemit FC = 30 FP 10 /^>seq[0-9]+ +\n/ FP /^VYITNLPPGVQKQELFDVKDTYFGEHGPVVRFNISRDDDDTQTGEASGFG\n/ FP /^EDAEAALENLRGIKINNRKLHI\n/ // ID ohmmindex-keep AB hmmer AA ohmmindex DL keep PP cp ../ohmm-own-keep4/myhmms myhmms CL myhmms FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI myhmms FC = 1287 FP /^LENG 250\n/ FI myhmms.gsi FZ = 304 FP /7LES_DROME/ // ID ohmmfetch-ex AB hmmer AA ohmmfetch CL ../ohmmindex-keep/myhmms 7LES_DROME/1799-1891 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI outfile.ohmmfetch FC = 277 FP /^NAME 7LES_DROME/1799-1891\n/ // ID oalistat-ex AB hmmer AA oalistat CL ../ohmmalign-keep/globins630.ali IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI globins630.oalistat FC = 14 FP /^Number of sequences: 630\n/ FP /^Average length: 145\.1\n/ FP /^Alignment length: 398\n/ FP /^Average identity: 39%\n/ FP /^Most distant seq: 11%\n/ // ####################################### # MEME # 1. Examples taken from meme-3.0.14/ README # 2. Data lives in: /emboss/emboss/test/data/memenew # 3. Do not use FZ lines as ememe & emast use temp # files with random names: these names are printed # to the output files. ####################################### ####################################### ID omeme-ex AB meme AA omeme CL -protein IN ../../data/memepep.dat IN IN 3 IN FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI carp_rhich.omeme FC = 359 FP /^MOTIF\s+1\s+width =\s+8\s+sites =\s+5\.0\n/ FP /MOTIF\s+2\s+width =\s+15\s+sites =\s+5\.0\n/ FP /^MOTIF\s+3\s+width =\s+16\s+sites =\s+5\.0\n/ FP 3 /^MOTIF/ // ####################################### # MEMENEW # 1. Examples taken from meme_4.0.0/ README # 2. Data lives in: /emboss/emboss/test/data/memenew # 3. Do not use FZ lines as ememe & emast use temp # files with random names: these names are printed # to the output files. ####################################### ID ememe-keep AB memenew RQ meme AA ememe DL keep CL ../../data/memenew/crp0.s -mod oops IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Multiple EM for Motif Elicitation\n/ FI stdout FC = 0 FI logo1.eps FZ = 13332 FP /^%%Pages: 0\n/ FI logo1.png FZ > 11500 FP /PNG/ FI logo_ssc1.png FZ > 12500 FP /PNG/ FI logo_ssc1.eps FZ = 13310 FP /^%%Pages: 0\n/ FI meme.html FC = 1416 FP /^ce1cg 1\.74e-03 1 105 [+]1 63 1\.91e-05 \n/ FP /^ce1cg \( 63\) TTTGATCGTTTTCAC 1 \n/ FI meme.fasta FC = 54 FP 18 /^>/ FI meme.txt FC = 272 FP /^ce1cg +1\.0000 105 ara +1\.0000 105 \n/ FI meme.xml FC = 860 FP /^\n/ FP /^\n/ FI meme.xsl FC = 1652 FP 2 /Find Genome Ontology terms/ // ID ememetext-ex AB memenew RQ meme AA ememetext CL ../../data/memenew/crp0.s -mod oops -revcomp ex.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI crp0.fasta FC = 54 FP 18 /^>/ FI ex.text FC = 272 FP /^ce1cg 1\.0000 105 ara 1\.0000 105 \n/ FP /^bglr1 1\.0000 105 crp 1\.0000 105 \n/ // ID ememetext-ex2 AB memenew RQ meme AA ememetext CL ../../data/memenew/crp0.s -mod oops -revcomp -w 20 ex2.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI crp0.fasta FC = 54 FP 18 /^>/ FI ex2.text FC = 282 FP /^ce1cg 1\.0000 105 ara 1\.0000 105 \n/ FP /^bglr1 1\.0000 105 crp 1\.0000 105 \n/ // ID ememetext-ex3 AB memenew RQ meme AA ememetext TI 300 CL ../../data/memenew/INO_up800.s -mod anr -revcomp CL -bfile ../../data/memenew/yeast.nc.6.freq ex3.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI ino_up800.fasta FC = 105 FP 7 /^>/ FI ex3.text FC = 237 FP /^CHO1 1\.0000 800 CHO2 1\.0000 800 \n/ FP /^FAS1 1\.0000 800 FAS2 1\.0000 800 \n/ // ID ememetext-ex4 AB memenew RQ meme AA ememetext CL ../../data/memenew/lipocalin.s -mod oops -maxw 20 -nmotifs 2 ex4.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI lipocalin.fasta FC = 22 FP 5 /^>/ FI ex4.text FC = 392 FP /^ICYA_MANSE 1\.0000 189 LACB_BOVIN 1\.0000 178 \n/ FP /^BBP_PIEBR 1\.0000 173 RETB_BOVIN 1\.0000 183 \n/ // ID ememetext-ex5 AB memenew RQ meme AA ememetext CL ../../data/memenew/farntrans5.s -mod anr -maxw 40 -maxsites 50 CL ex5.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI farntrans5.fasta FC = 40 FP 5 /^>/ FI ex5.text FC = 272 FP /^RAM1_YEAST 1\.0000 431 PFTB_RAT 1\.0000 437 \n/ FP /^BET2_YEAST 1\.0000 325 RATRABGERB 1\.0000 331 \n/ // ID ememetext-ex6 AB memenew RQ meme AA ememetext CL ../../data/memenew/farntrans5.s -mod anr -w 10 -maxsites 30 -nmotifs 3 CL ex6.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI farntrans5.fasta FC = 40 FP 5 /^>/ FI ex6.text FC = 557 FP /^RAM1_YEAST 1\.0000 431 PFTB_RAT 1\.0000 437 \n/ FP /^BET2_YEAST 1\.0000 325 RATRABGERB 1\.0000 331 \n/ // ID ememetext-ex7 AB memenew RQ meme AA ememetext CL ../../data/memenew/farntrans5.s -mod anr -maxw 12 -nsites 24 -nmotifs 3 CL ex7.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI farntrans5.fasta FC = 40 FP 5 /^>/ FI ex7.text FC = 615 FP /^RAM1_YEAST 1\.0000 431 PFTB_RAT 1\.0000 437 \n/ FP /^BET2_YEAST 1\.0000 325 RATRABGERB 1\.0000 331 \n/ // ID ememetext-ex8 AB memenew RQ meme AA ememetext TI 300 CL ../../data/memenew/adh.s -mod zoops -nmotifs 20 -evt 0.01 CL ex8.text IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 FI adh.fasta FC = 219 FP 33 /^>/ FI ex8.text FC = 1817 FP /^2BHD_STREX 1\.0000 255 3BHD_COMTE 1\.0000 253 \n/ FP /^ADH_DROME 1\.0000 255 AP27_MOUSE 1\.0000 244 \n/ // ID emast-ex AB memenew RQ meme AA emast ## PP cp ../ememe-keep/ex1.html . ## Cannot use output of ememe-keep test as input, ## because temporary sequence file named in /ememe-keep/ex1.html ## after "DATAFILE" will have been deleted. ## Instead use data/memenew/ex1.html which names the sequence file "crp0.s" ## which must be copied to the test directory. PP cp ../../data/memenew/crp0.s . CL ../../data/memenew/ex1.html ex1.out IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP /^Motif detection\n/ FI stdout FC = 0 FI ex1.out FC = 926 FP /^ LENGTH = 105 COMBINED P-VALUE = 4\.78e-04 E-VALUE = 0\.0086
\n/ FP /^1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG\n/ FI crp0.s FC = 54 FP /^>ce1cg\n/ // ####################################### # MSE ####################################### ID mse-ex AB mse AA mse CL ../../data/dna.msf msf::mse.msf IK :21 IK :1 up IK acgt:25 28 delete IK ----:exit FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FK stdout FZ > 2875 FP /exit/ FI mse.msf FC = 25 FP /^MSFM2 ACGTACGTACGTACGTACGTacgt\.\.\.\.ACGTACGTACGTACGTACGTAC\n/ FP 9 /^MSFM/ // ####################################### # MYEMBOSS # has no applications ####################################### ####################################### # MYEMBOSSDEMO ####################################### ID demoalign-check AB myembossdemo AQ demoalign CC No documentation, no example CL ../../data/dna.msf IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dna.demoalign FZ = 1273 FP 9 /^MSFM[1-3] +/ // ID demofeatures-check AB myembossdemo AQ demofeatures CC No documentation, no example IN test.out FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FZ = 632 FP /\A##gff-version 3\n/ FP 10 /^seq1\tdemofeature\t/ // ID demolist-check AB myembossdemo AQ demolist CC No documentation, no example CL ../../data/paamir.gff3 FI stderr FZ = 1227 FP 30 /^X13776\tEMBL\t[^ \t]/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demoreport-check AB myembossdemo AQ demoreport CC No documentation, no example CL tembl:x13776 test.out -rformat gff FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.out FZ = 2174 FP 10 /^X13776\tEMBL\t/ // ID demosequence-check AB myembossdemo AQ demosequence CC No documentation, no example, and no code CC Just checking it does nothing FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demostring-check AB myembossdemo AQ demostring CC No documentation, no example IN How long is a piece of string? FI stderr FZ = 874 FP /^first token 'How'\n/ FP /^second token 'long is a piece of string[?]'\n/ FP /Warning: Unknown date/time format fred\n/ FP 1 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID demostringnew-check AB myembossdemo AQ demostringnew CC No documentation, no example FI stderr FZ = 4062 FP 3 /str5: String 5 WITHSOMETEXTINABLOCK\n/ FP 0 /Error: / FP 0 /Died: / FI stdout FP /f1 \(from str3\): 0.500000\n/ FP /d1 \(from str4\): 0.500000\n/ // ID demotable-check AB myembossdemo AQ demotable CC No documentation, no example IN ../../data/paamir.gff3 FI stderr FC = 16 FP 7 /^type [a-zA-Z_']+ found/ FP /^type 'CDS' found 2 times\n/ FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID myseq-ex AB myembossdemo AQ myseq IN tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.myseq FC = 5 FP /^Usa: tembl-id:X13776\n/ FP /^Length: 2167\n/ // ID mytest-ex AB myembossdemo AQ mytest IN tembl:x13776 IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI x13776.mytest FC = 5 FP /^Usa: tembl-id:X13776\n/ FP /^Length: 2167\n/ // ####################################### # PHYLIP 3.5 ####################################### ID eclique-ex AB phylip AA eclique IN ../../data/evolution/clique.dat IN IN IN IN IN FI eclique.outfile FC = 31 FP /^Characters: \( 1 2 3 6\)\n/ FP /^ 2 1 3 6\n/ FI eclique.treefile FC = 1 FP /^\(\(\(Delta,Epsilon\),Gamma\),Alpha,Beta\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID econsense-ex AB phylip AA econsense IN ../../data/evolution/consense.dat IN IN IN FI econsense.outfile FC = 74 FP s /^ F\n I\n C\n/ FP /^\.\.\*\.\*\.\.\.\.\.\s+4\.00\n/ FI consense.treefile FC = 2 FP /^\(A:9\.0,\(\(E:9\.0,\(\(\(I:9\.0,F:9\.0\):9\.0,\(\(D:9\.0,\(J:9\.0,H:9\.0\):4\.0\)/ FP /\(J:9\.0,H:9\.0\):4\.0\):6\.0,C:9\.0\):6\.0\):2\.0,G:9\.0\):6\.0\):9\.0,\n/ FP /^B:9\.0\):9\.0\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^\n/ // ID econtml-ex AB phylip AA econtml IN ../../data/evolution/contml.dat IN IN IN IN IN IN IN IN IN FI econtml.outfile FC = 31 FP /^Ln Likelihood = 33\.29060\n/ FP /^ 3 Chinese 0\.00221 \( -0\.02034, 0\.03710\)\n/ FI econtml.treefile FC = 2 FP /^\(African:0\.08464,\(American:0\.02094,\(Australian:0\.05959,Chinese:0\.00221\)/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID econtrast-ex AB phylip AA econtrast IN ../../data/evolution/contrast.dat IN ../../data/evolution/contrast.tree IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI econtrast.outfile FC = 27 FP /^ 3\.9423 1\.7028\n/ FP /^ 1\.0000 0\.4319\n/ FP /^ 1\.0000 0\.6566\n/ // ID ednacomp-ex AB phylip AA ednacomp CL -stepoutput IN ../../data/evolution/dnacomp.dat IN IN IN IN IN FI ednacomp.outfile FC = 36 FP /total number of compatible sites is 11\.0\n/ FP / 0[!] 2 1 3 2 0 2 1 1 1\n/ FP / 0 [!] YYNYYYYYY\n/ FP /One most parsimonious tree found:\n/ FI ednacomp.treefile FC = 1 FP /\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ednadist-ex AB phylip AA ednadist IN ../../data/evolution/dnadist.dat IN IN IN IN FI ednadist.outfile FC = 6 FP / 5\n/ FP /^Alpha 0\.0000 0\.2997 0\.7820 1\.1716 1\.4617\n/ FI stderr FC = 10 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ednainvar-ex AB phylip AA ednainvar IN ../../data/evolution/dnainvar.dat IN FI ednainvar.outfile FC = 109 FP /^ AAAG 2\n/ FP /^ 1113 3\n/ FP /^ III: \(\(Alpha.*,Delta.*\),\(Beta.*,Gamma.*\)\)\n/ FP /^ III 0 - 0 = 0 1\.0000 no\n/ FP /^ Quadratic invariant = 4\.0\n/ FP 3 /^ Quadratic invariant =/ FP / Tree III: 5\.0\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / ## stdout has one blank line FI stdout FC = 1 FP /^\n/ // ID ednaml-ex AB phylip AA ednaml ## may need to play with the input file format for this one CL -categories -catnum 2 -catvals "1.0 3.2" -catprob "0.4 0.6" CL -lambda 1.5 -deflambda -printdata -progress IN ../../data/evolution/dnaml.dat IN IN IN IN IN IN IN IN FI ednaml.outfile FC = 67 FP /^ G 0\.24615\n/ FP /^ 2 3\.200 0\.600\n/ FP /^Ln Likelihood = -71\.831[0-9][0-9]\n/ FP /^ 2 +Beta +0\.00003 +\( +zero, +0\.41145\)\n/ FP /^ 1 +Gamma +1\.35995 +\( +zero, +3\.26620\) \*\*\n/ FP /^ 2122121111 212\n/ FI ednaml.treefile FC = 2 FP /^\(\(\(Epsilon:0\.00012,Delta:0\.30872\):3\.33144,Beta:0\.00012\):0\.08840,\n/ FP /^Gamma:1\.35995,Alpha:0\.24900\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 8 /^./ // ID ednamlk-ex AB phylip AA ednamlk CL -categories -catnum 2 -catvals "1.0 3.2" -catprob "0.4 0.6" CL -lambda 1.5 IN ../../data/evolution/dnaml.dat IN IN IN IN IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI ednamlk.outfile FC = 57 FP /Transition/transversion parameter = 1\.5230/ FP /^ \!\s+\+-------------?Gamma \n/ FP /^Ln Likelihood = -72\.40499\n/ FP /^ 3 4 3\.40036 3\.40036\n/ FI ednamlk.treefile FC = 2 FP /^\(\(Delta:0\.15834,Epsilon:0\.15834\):3\.40036,\(Gamma:0\.80621,\n/ FP /^\(Alpha:0\.17218,Beta:0\.17218\):0\.63403\):2\.75249\);\n/ // ID ednapars-ex AB phylip AA ednapars IN ../../data/evolution/dnapars.dat IN IN IN IN FI ednapars.outfile FC = 21 FP /^requires a total of 19\.000\n/ FP /^ \+--Epsilon.*\n/ FI ednapars.treefile FC = 1 FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ednapenny-ex AB phylip AA ednapenny IN ../../data/evolution/dnapenny.dat IN IN IN IN FI ednapenny.outfile FC = 207 FP /^ 9 trees in all found\n/ FP /^ \! \+-----6 \+-----Gamma2 \n/ FI ednapenny.treefile FC = 9 FP /^\(Alpha1,\(\(\(\(\(Delta,Epsilon\),Gamma2\),Gamma1\),\(Beta2,Beta1\)\),Alpha2\)\)\[0\.1111\];\n/ FP 3 /\(Gamma2,Gamma1\)/ FP 9 /\(Delta,Epsilon\),/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID edollop-ex AB phylip AA edollop IN ../../data/evolution/dollop.dat IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI edollop.outfile FC = 28 FP /^One most parsimonious tree found:\n/ FP 1 /^requires a total of 3\.000\n/ FI edollop.treefile FC = 1 FP /^\(Delta,\(Epsilon,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ // ID edolpenny-ex AB phylip AA edolpenny IN ../../data/evolution/dolpenny.dat IN IN IN IN FI edolpenny.outfile FC = 67 FP /^ 3 trees in all found\n/ FP 1 /^ \+--6 \+--5 \n/ FI edolpenny.treefile FC = 3 FP /^\(Delta,\(Epsilon,\(Gamma1,\(Alpha2,\(\(Beta2,Beta1\),Alpha1\)\)\)\)\)\[0\.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(Beta2,Beta1\),\(Alpha2,Alpha1\)\)\)\)\)\[0\.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(\(Beta2,Beta1\),Alpha2\),Alpha1\)\)\)\)\[0\.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID efactor-ex AB phylip AA efactor IN ../../data/evolution/factor.dat IN FI efactor.outfile FC = 5 FP /^ +4 +8\n/ FP /^Alpha 11100000\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 3 FP 1 /^./ // ID efitch-ex AB phylip AA efitch IN ../../data/evolution/fitch.dat IN IN IN IN FI efitch.outfile FC = 47 FP /^ 7 Populations\n/ FP /^Sum of squares = 0\.01417\n/ FP /^ 1 Mouse 0\.77028\n/ FP /^ 1 2 0\.41923\n/ FP /^ 2 Gibbon 0\.35442\n/ FI fitch.treefile FC = 2 FP /^\(Mouse:0\.77028,\(\(\(\(Human:0\.11417,Chimp:0\.15503\):0\.03705,\n/ FP /^Gorilla:0\.15677\):0\.01693,Orang:0\.29628\):0\.05289,Gibbon:0\.35442\):0\.41923,Bovine:0\.91632\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID egendist-ex AB phylip AA egendist IN ../../data/evolution/gendist.dat IN IN FI egendist.outfile FC = 6 FP /^ 5\n/ FP /^Chinese 0\.0807 0\.2347 0\.0000 0\.0539 0\.0633\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID ekitsch-ex AB phylip AA ekitsch IN ../../data/evolution/kitsch.dat IN IN FI ekitsch.outfile FC = 48 FP /^ 7 Populations\n/ FP /^Sum of squares = 0\.168\n/ FP /^ 6 Human 0\.13460 0\.81151\n/ FP /^ 5 6 0\.02776 0\.67691\n/ FP /^ 6 Chimp 0\.13460 0\.81151\n/ FI ekitsch.treefile FC = 3 FP /^\(\(\(\(\(\(Human:0\.13460,Chimp:0\.13460\):0\.02776,Gorilla:0\.16236\):0\.07664,\n/ FP /^Orang:0\.23900\):0\.06461,Gibbon:0\.30360\):0\.43105,Mouse:0\.73465\):0\.07686,\n/ FP /^Bovine:0\.81151\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID emix-ex AB phylip AA emix IN ../../data/evolution/mix.dat IN IN IN IN IN FI emix.outfile FC = 84 FP 4 /^requires a total of 9\.000\n/ FP /^ 4 trees in all found\n/ FP 2 /^--1 \! \+--Delta +\n/ FI emix.treefile FC = 4 FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0\.2500\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.2500\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0\.2500\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0\.2500\];\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eneighbor-ex AB phylip AA eneighbor IN ../../data/evolution/neighbor.dat IN IN IN IN IN FI eneighbor.outfile FC = 40 FP /^ 7 Populations\n/ FP /^ 1 Mouse 0\.76891\n/ FP /^ 2 1 0\.42027\n/ FP /^ 2 Gibbon 0\.35793\n/ FI eneighbor.treefile FC = 2 FP /\(Gorilla:0\.15393,\(Chimp:0\.1516[78],Human:0\.11753\):0\.03982/ FP /^Mouse:0\.76891\):0\.42027,Gibbon:0\.35793\):0\.04648/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID epenny-ex AB phylip AA epenny IN ../../data/evolution/penny.dat IN IN IN IN FI epenny.outfile FC = 66 FP /^ 3 trees in all found\n/ FP 3 /^ remember: this is an unrooted tree\!\n/ FP /^ \! \+-----Alpha2 \n/ FI epenny.treefile FC = 3 FP /^\(Alpha1,\(\(Alpha2,\(\(Epsilon,Delta\),Gamma1\)\),\(Beta2,Beta1\)\)\)\[0\.3333\];\n/ FP /^\(Alpha1,\(Alpha2,\(\(\(Epsilon,Delta\),Gamma1\),\(Beta2,Beta1\)\)\)\)\[0\.3333\];\n/ FP /^\(Alpha1,\(\(Alpha2,\(Beta2,Beta1\)\),\(\(Epsilon,Delta\),Gamma1\)\)\)\[0\.3333\];\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^\n/ // ID eprotdist-ex AB phylip AA eprotdist IN ../../data/evolution/protdist.dat IN IN FI eprotdist.outfile FC = 6 FP /^Gamma 0\.88304 0\.45192 0\.00000 1\.30693 1\.21582\n/ FI stderr FC = 6 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eprotpars-ex AB phylip AA eprotpars IN ../../data/evolution/protpars.dat IN IN IN IN FI eprotpars.outfile FC = 58 FP /^ 3 trees in all found\n/ FP 1 /^ \! \+--Beta \n/ FP 2 /^ \! +\+-+Beta +\n/ FI eprotpars.treefile FC = 3 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID erestml-ex AB phylip AA erestml IN ../../data/evolution/restml.dat IN IN IN IN FI erestml.outfile FC = 42 FP /^Ln Likelihood = -40\.3585[78]\n/ FP /^ 1 Gamma 0\.11430 \( 0\.11177, 0\.11683\) \*\*\n/ FI erestml.treefile FC = 2 FP /^\(\(Epsilon:0\.00005,Delta:0\.01458\):0\.05855,\(Gamma:0\.11430,\n/ FP /^Beta:0\.00008\):0\.00002,Alpha:0\.02468\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eseqboot-ex AB phylip AA eseqboot IN ../../data/evolution/seqboot.dat IN IN IN IN IN FI eseqboot.outfile FC = 600 FP 11 /^Alpha AAAAAA\n/ FP 17 /^Beta AAACCC\n/ FP 25 /^\S+ +AAACCC\n/ FP 100 /^Alpha/ FI stderr FC = 11 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ####################################### # PHYLIP 3.6 ####################################### ID fclique-ex AB phylipnew AA fclique IN ../../data/evolution/clique.dat IN FI clique.fclique FC = 31 FP /^Characters: \( 1 2 3 6\)\n/ FP /^ 2 1 3 6\n/ FI clique.treefile FC = 1 FP /^\(\(\(Delta,Epsilon\),Gamma\),Alpha,Beta\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 7 FP 3 /^./ // ID fclique-all AB phylipnew AA fclique CL -ancfile ../../data/evolution/clique.ancestral CL -factorfile ../../data/evolution/clique.factors CL -weights ../../data/evolution/clique.weights IN ../../data/evolution/clique.dat IN FI clique.fclique FC = 35 FP /^ 11223 4\n/ FP /^Actual Characters: \( 1 4\)\n/ FP /^Binary Characters: \( 1 2 6\)\n/ FP 1 /Tree and binary characters:/ FI clique.treefile FC = 1 FP /^\(\(\(\(Alpha,Beta\),Gamma\),Epsilon\),Delta\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 7 FP 3 /^./ // ID fconsense-ex AB phylipnew AA fconsense IN ../../data/evolution/consense.dat IN FI consense.fconsense FC = 77 FP /^ 10\. C\n/ FP /^\.\.\*\.\*\.\.\.\.\.\s+4\.00\n/ FI consense.treefile FC = 2 FP /^E:9\.00\):9\.00,B:9\.00\):9\.00,A:9\.00\);\n/ FP /\(\(H:9\.00,J:9\.00\):4\.00,D:9\.00\)/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 7 FP 3 /^./ // ID fcontml-ex AB phylipnew AA fcontml CL -printdata IN ../../data/evolution/contml.dat IN IN FI contml.fcontml FC = 67 FP /^Ln Likelihood = 38\.7191[0-9]\n/ FP /^ 2 Chinese 0\.00208822 \( -0\.00960622, 0\.02017433\)\n/ FI contml.treefile FC = 2 FP /\(African:0\.09693444,\(Australian:0\.05247405,\(American:0\.03806240,Chinese:0\.00208822\):0\.00945315\):0\.02252816,/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP 9 /^./ // ID fcontrast-ex AB phylipnew AA fcontrast IN ../../data/evolution/contrast.dat IN ../../data/evolution/contrast.tree IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI contrast.fcontrast FC = 19 FP /^ 3\.9423 1\.7028\n/ FP /^ 1\.0000 0\.4319\n/ FP /^ 1\.0000 0\.6566\n/ FI stdout FC = 5 FP 2 /^./ // ID fdiscboot-ex AB phylipnew AA fdiscboot CL -seed 3 IN ../../data/evolution/discboot.dat IN IN IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ FI discboot.ancfile FZ = 0 FI discboot.factfile FZ = 0 FI discboot.mixfile FZ = 0 FI discboot.fdiscboot FC = 600 FP 100 /^Alpha/ FP 10 /^Alpha 111100\n/ // ID fdnacomp-ex AB phylipnew AA fdnacomp CL -ancseq -stepbox -printdata IN ../../data/evolution/dnacomp.dat IN IN IN FI dnacomp.fdnacomp FC = 62 FP /total number of compatible sites is 11\.0\n/ FP / 4 Epsilon maybe GGGATCTCGG CCC\n/ FP / 0[|] 2 1 3 2 0 2 1 1 1\n/ FP / 0 [!] YYNYYYYYY\n/ FP /One most parsimonious tree found:\n/ FI dnacomp.treefile FC = 1 FP /\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 11 /^./ // ID fdnacomp-ex2 AB phylipnew AA fdnacomp IN ../../data/evolution/dnacomp.dat IN ../../data/evolution/dnacomptree.dat IN IN FI dnacomp.fdnacomp FC = 23 FP /^User-defined tree:\n/ FP /^total number of compatible sites is 11\.0\n/ FI dnacomp.treefile FC = 1 FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FP 2 /^./ // ID fdnadist-ex AB phylipnew AA fdnadist IN ../../data/evolution/dnadist.dat IN IN FI dnadist.fdnadist FC = 6 FP / 5\n/ FP /^Alpha 0\.000000 0\.303900 0\.857544 1\.158927 1\.542899\n/ FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP 8 /^./ // ID fdnainvar-ex AB phylipnew AA fdnainvar CL -printdata IN ../../data/evolution/dnainvar.dat IN IN FI dnainvar.fdnainvar FC = 120 FP /^ AAAG 2\n/ FP /^ 1113 3\n/ FP /^ III: \(\(Alpha,Delta\),\(Beta,Gamma\)\)\n/ FP /^ III 0 - 0 = 0 1\.0000 no\n/ FP /^ Quadratic invariant = 4\.0\n/ FP 3 /^ Quadratic invariant =/ FP / Tree III: 5\.0\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID fdnaml-ex AB phylipnew AA fdnaml CL -printdata CL -ncategories 2 -categories "1111112222222" -rate "1.0 2.0" CL -gamma h CL -nhmmcategories 5 -hmmrates "0.264 1.413 3.596 7.086 12.641" CL -hmmprobabilities "0.522 0.399 0.076 0.0036 0.000023" CL -lambda 1.5 CL -weight "0111111111110" IN ../../data/evolution/dnaml.dat IN IN FI dnaml.fdnaml FC = 91 FP /^ 1 0\.264 0\.522\n/ FP /^ 2 2\.000\n/ FP /^Ln Likelihood = -57\.87892\n/ FP /^ 1 Alpha 0\.26766 \( zero, 0\.80513\) \*\n/ FP /^ 1132121111 211\n/ FI dnaml.treefile FC = 2 FP /^\(\(\(Epsilon:0\.00006,Delta:0\.27319\):7\.59821,Beta:0\.00006\):0\.04687,\n/ FP /^Gamma:0\.95677,Alpha:0\.26766\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 53 FP 45 /^./ // ID fdnaml-ex2 AB phylipnew AA fdnaml CL -printdata CL -njumble 3 -seed 3 IN ../../data/evolution/dnaml.dat IN IN FI dnaml.fdnaml FC = 57 FP /^ A 0\.24615\n/ FP /^Ln Likelihood = -72\.25088\n/ FP /^ 1 Epsilon 0\.00006 \( zero, 0\.34299\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 67 FP 57 /^./ FI dnaml.treefile FC = 2 FP /^Gamma:1\.01651,Alpha:0\.20745\);\n/ // ID fdnamlk-ex AB phylipnew AA fdnamlk CL -printdata CL -ncategories 2 -categories "1111112222222" -rate "1.0 2.0" CL -gamma h CL -nhmmcategories 5 -hmmrates "0.264 1.413 3.596 7.086 12.641" CL -hmmprobabilities "0.522 0.399 0.076 0.0036 0.000023" CL -lambda 1.5 CL -weight "0111111111110" IN ../../data/evolution/dnaml.dat IN IN CC likelihood value differs on Linux. FI dnaml.fdnamlk FC = 90 FP /^ 1 0\.264 0\.522\n/ FP /^ 2 2\.000\n/ FP /^Ln Likelihood = -57\.98242\n/ FP /^ 2 Gamma 4\.15060 0\.55971\n/ FP /^ 1132121111 211\n/ FI dnaml.treefile FC = 2 FP /^\(\(Epsilon:0\.13456,Delta:0\.13456\):4\.01604,\(Gamma:0\.55971,\n/ FP /^\(Beta:0\.15731,Alpha:0\.15731\):0\.40240\):3\.59089\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP 9 /^./ // ID fdnamove-ex AB phylipnew AA fdnamove IN ../../data/evolution/dnamove.dat IN IN Q IN Y FI dnamove.treefile FC = 1 FP /^\(Epsilon,\(Delta,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 20 FP 14 /^./ // ID fdnapars-ex AB phylipnew AA fdnapars IN ../../data/evolution/dnapars.dat IN IN FI dnapars.fdnapars FC = 30 FP /^requires a total of 19\.000\n/ FP /^ 3 Epsilon 0\.096154\n/ FI dnapars.treefile FC = 2 FP /^\(\(\(Epsilon:0\.09615,Delta:0\.13462\):0\.48718,Gamma:0\.27564\):0\.21795,\n/ FP /^Beta:0\.07692,Alpha:0\.17308\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 21 FP 15 /^./ // ID fdnapenny-ex AB phylipnew AA fdnapenny IN ../../data/evolution/dnapenny.dat IN FI dnapenny.fdnapenny FC = 207 FP /^ 9 trees in all found\n/ FP /^ 1 \+-----4 \+--Epsilon \n/ FI dnapenny.treefile FC = 9 FP /^\(Alpha1,\(\(Alpha2,\(\(Epsilon,Delta\),\(Gamma2,Gamma1\)\)\),\(Beta2,Beta1\)\)\)\[0\.1111\];\n/ FP 3 /\(Gamma2,Gamma1\)/ FP 6 /\(Epsilon,Delta\),/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 18 FP 14 /^./ // ID fdollop-ex AB phylipnew AA fdollop IN ../../data/evolution/dollop.dat IN IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI dollop.fdollop FC = 24 FP /^One most parsimonious tree found:\n/ FP 1 /^requires a total of 3\.000\n/ FI dollop.treefile FC = 1 FP /^\(Delta,\(Epsilon,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stdout FC = 19 FP 13 /^./ // ID fdolmove-ex AB phylipnew AA fdolmove IN ../../data/evolution/dolmove.dat IN IN Q IN Y FI dolmove.treefile FC = 1 FP /^\(Epsilon,\(Delta,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 24 FP 15 /^./ // ID fdolpenny-ex AB phylipnew AA fdolpenny IN ../../data/evolution/dolpenny.dat IN FI dolpenny.fdolpenny FC = 63 FP /^ 3 trees in all found\n/ FP 1 /^ \+--6 \+--5 \n/ FI dolpenny.treefile FC = 3 FP /^\(Delta,\(Epsilon,\(Gamma1,\(Alpha2,\(\(Beta2,Beta1\),Alpha1\)\)\)\)\)\[0\.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(Beta2,Beta1\),\(Alpha2,Alpha1\)\)\)\)\)\[0\.3333\];\n/ FP /^\(Delta,\(Epsilon,\(Gamma1,\(\(\(Beta2,Beta1\),Alpha2\),Alpha1\)\)\)\)\[0\.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 13 FP 9 /^./ // ID fdrawgram-ex AB phylipnew AA fdrawgram CL -previewer n IN ../../data/evolution/drawgram.tree IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 12 FP 8 /^./ FI drawgram.fdrawgram FC = 76 FP /\%\!PS-Adobe-2\.0\n/ FP 5 /show\n/ // ID fdrawtree-ex AB phylipnew AA fdrawtree CL -previewer n IN ../../data/evolution/drawgram.tree IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 12 FP 8 /^./ FI drawgram.fdrawtree FC = 67 FP /\%\!PS-Adobe-2\.0\n/ FP 5 /show\n/ // ID ffactor-ex AB phylipnew AA ffactor CC output fails to match documentation, also reports failure IN ../../data/evolution/factor.dat IN FI factor.ffactor FC = 5 FP /^ +4 +5\n/ FP /^Alpha CA00\#\n/ FP /^Beta BB01\%\n/ FP /^Gamma AB12\#\n/ FP /^Epsilon CA01\$\n/ FI factor.factor FC = 0 FI factor.ancestor FC = 0 FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ffitch-ex AB phylipnew AA ffitch IN ../../data/evolution/fitch.dat IN IN FI fitch.ffitch FC = 50 FP /^ 7 Populations\n/ FP /^Sum of squares = 0\.01375\n/ FP /^Average percent standard deviation = 1\.85418\n/ FP /^ 1 Mouse 0\.76985\n/ FP /^ 1 2 0\.41983\n/ FP /^ 2 Gibbon 0\.35537\n/ FI fitch.treefile FC = 2 FP /^\(Mouse:0\.76985,\(\(\(\(Human:0\.11449,Chimp:0\.15471\):0\.03695,\n/ FP /^Gorilla:0\.15680\):0\.02121,Orang:0\.29209\):0\.04986,Gibbon:0\.35537\):0\.41983,Bovine:0\.91675\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 11 /^./ // ID ffreqboot-ex AB phylipnew AA ffreqboot CL -seed 3 IN ../../data/evolution/freqboot.dat IN FI freqboot.ffreqboot FC = 1700 FP 100 /^European/ FP 57 /^European 0\.28680 / FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID fgendist-ex AB phylipnew AA fgendist IN ../../data/evolution/gendist.dat IN FI gendist.fgendist FC = 6 FP /^ 5\n/ FP /^Chinese 0\.080749 0\.234698 0\.000000 0\.053879 0\.063275\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 11 FP 8 /^./ // ID fkitsch-ex AB phylipnew AA fkitsch IN ../../data/evolution/kitsch.dat IN IN FI kitsch.fkitsch FC = 49 FP /^ 7 Populations\n/ FP /^Sum of squares = 0\.107\n/ FP /^Average percent standard deviation = 5\.16213\n/ FP /^ 6 Human 0\.13460 0\.81285\n/ FP /^ 5 6 0\.02836 0\.67825\n/ FP /^ 6 Chimp 0\.13460 0\.81285\n/ FI kitsch.treefile FC = 3 FP /^\(\(\(\(\(\(Human:0\.13460,Chimp:0\.13460\):0\.02836,Gorilla:0\.16296\):0\.07638,\n/ FP /^Orang:0\.23933\):0\.06639,Gibbon:0\.30572\):0\.42923,Mouse:0\.73495\):0\.07790,\n/ FP /^Bovine:0\.81285\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 19 FP 14 /^./ // ID fmix-ex AB phylipnew AA fmix IN ../../data/evolution/mix.dat IN IN FI mix.fmix FC = 86 FP 4 /^requires a total of 9\.000\n/ FP /^ 4 trees in all found\n/ FP 2 /^--1 \! \+--Delta +\n/ FI mix.treefile FC = 4 FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0\.2500\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.2500\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0\.2500\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0\.2500\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 11 /^./ // ID fmix-ex2 AB phylipnew AA fmix CL -printdata -ancfile ../../data/evolution/mixancfile.dat IN ../../data/evolution/mix.dat IN IN FI mix.fmix FC = 46 FP /^ Ancestral states:\n/ FP /^ 001\?\? 1\n/ FP /^One most parsimonious tree found:\n/ FP /^requires a total of 8\.000\n/ FI mix.treefile FC = 1 FP /^\(Delta,\(Epsilon,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 11 /^./ // ID fmove-ex AB phylipnew AA fmove IN ../../data/evolution/move.dat IN IN Q IN Y FI move.treefile FC = 1 FP /^\(Epsilon,\(Delta,\(Gamma,\(Beta,Alpha\)\)\)\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 15 /^./ // ID fneighbor-ex AB phylipnew AA fneighbor IN ../../data/evolution/neighbor.dat IN FI neighbor.fneighbor FC = 43 FP /^ 7 Populations\n/ FP /^ \! \! \+--------Gorilla \n/ FP /^ 1 Mouse 0\.76891\n/ FP /^ 1 2 0\.42027\n/ FP /^ 2 Gibbon 0\.35793\n/ FI neighbor.treefile FC = 2 FP /^\(Mouse:0\.76891,\(Gibbon:0\.35793,\(Orang:0\.28469,\(Gorilla:0\.15393,\n/ FP /^\(Chimp:0\.15168,Human:0\.11752\):0\.03982\):0\.02696\):0\.04648\):0\.42027,Bovine:0\.91769\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 9 /^./ // ID fpars-ex AB phylipnew AA fpars IN ../../data/evolution/pars.dat IN IN FI pars.fpars FC = 30 FP /^One most parsimonious tree found:\n/ FP /^requires a total of 8\.000\n/ FP /^ 3 Epsilon 0\.00\n/ FP /^ 3 Delta 3\.00\n/ FI pars.treefile FC = 1 FP /^\(\(\(Epsilon:0\.00,Delta:3\.00\):2\.00,Gamma:0\.00\):1\.00,Beta:2\.00,Alpha:0\.00\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 21 FP 15 /^./ // ID fpenny-ex AB phylipnew AA fpenny IN ../../data/evolution/penny.dat IN FI penny.fpenny FC = 70 FP /^ 3 trees in all found\n/ FP 3 /^ remember: this is an unrooted tree\!\n/ FP /^ \! \+-----Alpha2 \n/ FI penny.treefile FC = 3 FP /^\(Alpha1,\(\(Alpha2,\(\(Epsilon,Delta\),Gamma1\)\),\(Beta2,Beta1\)\)\)\[0\.3333\];\n/ FP /^\(Alpha1,\(Alpha2,\(\(\(Epsilon,Delta\),Gamma1\),\(Beta2,Beta1\)\)\)\)\[0\.3333\];\n/ FP /^\(Alpha1,\(\(Alpha2,\(Beta2,Beta1\)\),\(\(Epsilon,Delta\),Gamma1\)\)\)\[0\.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 16 FP 12 /^./ // ID fproml-ex AB phylipnew AA fproml IN ../../data/evolution/proml.dat IN IN FI proml.fproml FC = 36 FP /^Ln Likelihood = -131\.55052\n/ FP /^ 1------2 \+------------Delta \n/ FP /^ 1 +Alpha +0\.31006 +\( +zero, +0\.66806\) \*\*\n/ FI proml.treefile FC = 2 FP /^\(Beta:0\.00010,\(\(Epsilon:0\.00010,Delta:0\.41176\):1\.00907,\n/ FP /^Gamma:0\.68569\):0\.22206,Alpha:0\.31006\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP 9 /^./ // ID fpromlk-ex AB phylipnew AA fpromlk IN ../../data/evolution/promlk.dat IN IN FI promlk.fpromlk FC = 38 FP /^Ln Likelihood = -134\.70332\n/ FP /^ root 3 \n/ FP /^ 3 4 0\.66464 0\.66464\n/ FP /^ 4 Epsilon 0.85971 0.19507\n/ FI promlk.treefile FC = 2 FP /^\(\(Epsilon:0\.19507,Delta:0\.19507\):0\.66464,\(Gamma:0\.48551,\n/ FP /^\(Beta:0\.15763,Alpha:0\.15763\):0\.32788\):0\.37420\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP 9 /^./ // ID fprotdist-ex AB phylipnew AA fprotdist IN ../../data/evolution/protdist.dat IN FI protdist.fprotdist FC = 6 FP /^Gamma 0.628142 0.377406 0.000000 0.979550 0.866781\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 12 FP 8 /^./ // ID fprotpars-ex AB phylipnew AA fprotpars IN ../../data/evolution/protpars.dat IN IN FI protpars.fprotpars FC = 61 FP /^ 3 trees in all found\n/ FP 1 /^ \! \+--Beta \n/ FP 2 /^ \! +\+-+Beta +\n/ FI protpars.treefile FC = 3 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 19 FP 13 /^./ // ID fprotpars-ex2 AB phylipnew AA fprotpars CL -njumble 3 -seed 3 CL -printdata CL -ancseq CL -whichcode m CL -stepbox CL -outgrno 2 CL -thresh -threshold 3 IN ../../data/evolution/protpars.dat IN IN FI protpars.fprotpars FC = 137 FP /^ 3 trees in all found\n/ FP 3 /^requires a total of 14\.000\n/ FI protpars.treefile FC = 3 FP /^\(Beta,\(Gamma,\(\(Epsilon,Delta\),Alpha\)\)\)\[0\.3333\];\n/ FP /^\(Beta,\(\(\(Epsilon,Delta\),Gamma\),Alpha\)\)\[0\.3333\];\n/ FP /^\(Beta,\(\(Epsilon,Delta\),\(Gamma,Alpha\)\)\)\[0\.3333\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 43 FP 31 /^./ // ID fprotpars-ex3 AB phylipnew AA fprotpars CL -njumble 3 -seed 3 IN ../../data/evolution/protpars2.dat IN IN FI protpars2.fprotpars FC = 435 FP /^Data set # 1:\n/ FP /^ 3 trees in all found\n/ FP 3 /^requires a total of 25\.000\n/ FP /^Data set # 2:\n/ FP /^ 15 trees in all found\n/ FP 15 /^requires a total of 14\.000\n/ FP /^Data set # 3:\n/ FP /^ 5 trees in all found\n/ FP 5 /^requires a total of 24\.000\n/ FI protpars2.treefile FC = 23 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.3333\];\n/ FP /^\(\(Gamma,\(Delta,\(Epsilon,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Delta,Gamma\),\(Epsilon,Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Delta,\(Epsilon,Gamma\)\),Beta\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Epsilon,\(\(Delta,Gamma\),Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Epsilon,\(Delta,Gamma\)\),Beta\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Delta,\(Gamma,\(Epsilon,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Delta,\(\(Epsilon,Gamma\),Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Delta,\(Epsilon,\(Gamma,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Epsilon,\(Delta,\(Gamma,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Gamma,\(Delta,\(Epsilon,Beta\)\)\),Alpha\)\[0\.2000\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.2000\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0\.2000\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.2000\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.2000\];\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 129 FP 94 /^./ // ID fprotpars-ex4 AB phylipnew AA fprotpars CL -option IN ../../data/evolution/protpars.dat IN IN ../../data/evolution/protparswts.dat IN IN IN IN IN IN IN IN IN IN IN IN FI protpars.fprotpars FC = 342 FP /^Weights set # 1:\n/ FP /^ 3 trees in all found\n/ FP 3 /^requires a total of 14\.000\n/ FP /^Weights set # 2:\n/ FP /^ 15 trees in all found\n/ FP 15 /^requires a total of 2\.000\n/ FI protpars.treefile FC = 18 FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.3333\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.3333\];\n/ FP /^\(\(Gamma,\(Delta,\(Epsilon,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Epsilon,Gamma\),\(Delta,Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Gamma,\(\(Epsilon,Delta\),Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Epsilon,\(Gamma,\(Delta,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Gamma,\(Epsilon,\(Delta,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Delta,Gamma\),\(Epsilon,Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Delta,\(Epsilon,Gamma\)\),Beta\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(\(Epsilon,Delta\),Gamma\),Beta\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Epsilon,\(\(Delta,Gamma\),Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Epsilon,\(Delta,Gamma\)\),Beta\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Delta,\(Gamma,\(Epsilon,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Delta,\(\(Epsilon,Gamma\),Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(\(Epsilon,Delta\),\(Gamma,Beta\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Delta,\(Epsilon,\(Gamma,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FP /^\(\(Epsilon,\(Delta,\(Gamma,Beta\)\)\),Alpha\)\[0\.0667\];\n/ FI stderr FC = 8 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 41 FP 27 /^./ // ID frestboot-ex AB phylipnew AA frestboot CL -seed 3 IN ../../data/evolution/restboot.dat IN FI restboot.frestboot FC = 600 FP 100 /^Gamma/ FP 3 /^Gamma \-\+\-\-\-\+\+\+\+\+\ \+\+\+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID frestdist-ex AB phylipnew AA frestdist IN ../../data/evolution/restdist.dat IN FI restdist.frestdist FC = 6 ## This is what we get from a fixed frestdist ## phylip-3.6b restdist has the same valgrind error ## Need to check current release to see if it is fixed FP /^Gamma 0\.107681 0\.107681 0\.000000 0\.192466 0\.207319\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 14 FP 9 /^./ // ID frestml-ex AB phylipnew AA frestml IN ../../data/evolution/restml.dat IN IN FI restml.frestml FC = 41 FP /^Ln Likelihood = -40\.47082\n/ FP /^ 1 Gamma 0\.10794 \( 0\.01144, 0\.21872\) \*\*\n/ FI restml.treefile FC = 2 FP /^\(Gamma:0\.10794,\(Beta:0\.00100,\(Epsilon:0\.00022,\n/ FP /^Delta:0\.01451\):0\.05878\):0\.01244,Alpha:0\.01244\);\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 15 FP 10 /^./ // ID fretree-ex AB phylipnew AA fretree CC First prompt only needed until it can read CC the number of species from the input tree IN 10 IN ../../data/evolution/retree.dat IN IN Q IN Y IN U FI retree.treefile FC = 2 FP /^\(\(\(\(\(\(\(Human,Chimp\),Gorilla\),Orang\),Gibbon\),\(Barbary_Ma,\(Crab-e\._Ma,\n/ FP /^\(Rhesus_Mac,Jpn_Macaq\)\)\)\),Squir\._Mon\),\(\(Tarsier,Lemur\),Bovine\),Mouse\);\n/ FI stderr FC = 4 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 27 FP 23 /^./ // ID fseqboot-ex AB phylipnew AA fseqboot CL -seed 3 IN ../../data/evolution/seqboot.dat IN FI seqboot.fseqboot FC = 600 FP 7 /^Alpha AAAAAA\n/ FP 14 /^Beta AAACCC\n/ FP 21 /^\S+ +AAACCC\n/ FP 100 /^Alpha/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID fseqbootall-ex AB phylipnew AA fseqbootall CL -seed 3 IN ../../data/evolution/seqboot.dat IN FI seqboot.fseqbootall FC = 600 FP 7 /^Alpha AAAAAA\n/ FP 14 /^Beta AAACCC\n/ FP 21 /^\S+ +AAACCC\n/ FP 100 /^Alpha/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 23 FP 18 /^./ // ID ftreedist-ex AB phylipnew AA ftreedist IN ../../data/evolution/treedist.dat IN FI treedist.ftreedist FC = 11 FP /Trees 3 and 4: 3\.162278e\-01/ FP 6 /Trees \d+ and \d+:\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedist-ex2 AB phylipnew AA ftreedist CL -dtype s IN ../../data/evolution/treedist2.dat IN FI treedist2.ftreedist FC = 11 FP /Trees 1 and 2: 4/ FP 6 /Trees \d+ and \d+:\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedist-sparse AB phylipnew AA ftreedist CL -style s IN ../../data/evolution/treedist.dat IN IN FI treedist.ftreedist FC = 6 FP /3 4 3\.162278e\-01/ FP 6 /\d+\s+\d+\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedist-listall AB phylipnew AA ftreedist CL -dtype s IN ../../data/evolution/treedist.dat IN FI treedist.ftreedist FC = 11 FP /Trees 11 and 12: 10\n/ FP 6 /Trees \d+ and \d+:\s+\d+/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 5 FP 2 /^./ // ID ftreedistpair-ex AB phylipnew AA ftreedistpair CL -style s IN ../../data/evolution/treedist.dat IN ../../data/evolution/treedist.dat IN FI treedist.ftreedistpair FC = 288 FP /^1 14 2\.000000e-01\n/ FP /^2 13 2\.000000e-01\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP 1 /^./ // ####################################### # TOPO ####################################### ID topo-ex AB topo AA topo CL tsw:aqp1_human -signa -prol=UM -cys=cg -gly=sr -acid=dr CL -basic=db -ohaa=da -araa=dg -graph ps IN 18 35 49 67 94 115 136 156 165 184 211 232 IN n IN 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 1 FP /^Created topo\.ps\n/ FI topo.ps FZ > 950000 FP /^%%Title: PLplot Graph\n/ // ####################################### # APPENDIXD ####################################### ID crystalball-ex AB appendixd AA crystalball CL -competition -rdtime -rdcost -animalstudies -clinicaltrials CL -fdaproblems -fdatime -profit -everythingelse IN tembl:x65923 IN FI x65923.crystalball FC = 9 FP 9 /:/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ####################################### # VIENNA ####################################### ID ovrnaalifold-ex AB vienna AA ovrnaalifold IN ../../data/ecoli6s.fasta IN FI ecoli6s.ovrnaalifold FC = 2 FP /\(-56\.91 \= -48\.71 \+ -8\.20\) \n/ FP /^\.\.\.\.\(\(\(\(\(\(\(\(\(\(\(\.\(\(\(\.\..*\)\)\.\)\)\)\)\)\)\.\.\.\.\. / FI ecoli6s.ssps FC = 523 FP /^%%Pages: 1\n/ FI ecoli6s.alirnaps FC = 1005 FP /^showpage\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaalifoldpf-ex AB vienna AA ovrnaalifoldpf IN ../../data/ecoli6s.fasta IN FI ecoli6s.ssps FC = 523 FP /^%%Pages: 1\n/ FI ecoli6s.ps FC = 330 FP /^%%Pages: 1\n/ FI ecoli6s.alirnaps FC = 1005 FP /^showpage\n/ FI ecoli6s.ovrnaalifoldpf FC = 177 FP /\(-56\.91 \= -48\.71 \+ -8\.20\) \n/ FP /^\.\.\.\.\(\(\(\(\(\(\(\(\(\(\(\.\(\(\(\.\..*\)\)\.\)\)\)\)\)\)\.\.\.\.\. / FP /^\.\.\.\.\(\(.*\.\.\{\.\(\(\..*\)\)\.\.\.\.\. \[-59\.30\]\n/ FP /^ frequency of mfe structure in ensemble 0\.0206905\n/ FP /^7 sequences; length of alignment 203\n/ FP /^ 64 142 0 100\.0\% 0\.000 CG:1 GC:4 UG:1 UA:1 \n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnacofold-ex AB vienna AA ovrnacofold ## Example from Algorithms Mol Biol. 2006; 1: 3. ## Partition function and base pairing probabilities of RNA heterodimers ## Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, ## Peter F Stadler and Ivo L Hofacker IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN FI red.ovrnacofold FC = 2 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\(\(\(\(\.\.\&\.\.\)\)\)\)\(\(\(\.\.\.\.\)\)\)\. \( -4\.40\)\n/ FI red.ssps FC = 139 FP /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnacofoldconc-ex AB vienna AA ovrnacofoldconc IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN ../../data/cofold-conc.dat IN FI red.ovrnacofoldconc FC = 11 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\(\(\(\(\.\.\&\.\.\)\)\)\)\(\(\(\.\.\.\.\)\)\)\. \( -4\.40\)\n/ FP /^-5.838299\t+1.006546\t+-16.231717\t+-0.003662\t+-4.266495\n/ FI red.ssps FC = 139 FP /^%%Pages: 1\n/ FI red.aps FC = 119 FP /^%%Pages: 1\n/ FI red.aaps FC = 158 FP /^%%Pages: 1\n/ FI red.abps FC = 205 FP /^%%Pages: 1\n/ FI red.bps FC = 135 FP /^%%Pages: 1\n/ FI red.bbps FC = 148 FP /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnacofoldpf-ex AB vienna AA ovrnacofoldpf IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN FI red.ovrnacofoldpf FC = 4 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\(\(\(\(\.\.\&\.\.\)\)\)\)\(\(\(\.\.\.\.\)\)\)\. \( -4\.40\)\n/ FP /^\.\.\.\.\(\(\(\(\,\.\&\.\.\)\)\)\}\(\(\(\.\.\.\.\)\)\)\. \[ -5\.88\]\n/ FP /^ frequency of mfe structure in ensemble 0\.279848 , delta G binding\= -1\.57\n/ FI red.ps FC = 203 FP /^%%Pages: 1\n/ FI red.ssps FC = 139 FP /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnadistance-ex AB vienna AA ovrnadistance CL -distance 'f,h' -doalignment IN ../../data/rna4.fold IN FI rna4.ovrnadistance FC = 7 FP /^f: 26 \n/ FP /^h: 32 \n/ FP /^\(_____\(\.\(\(\(__\(\(\(\(\.\.\.\.\._____\)\)\)\)_\)\)\)\.\)\)\.\.\.\.\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\)\)\.\n/ FP /^_\.\.\.\.\.\(_\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\.\.\.\.\)\)\)\)\.\)\)\)_\)_\.\.\.\.__\.__\(\(\(\.\.\.\._\)\)\)_\.___\n/ FP /^\(____\(\(U1\)\(\(U5_\)P7\)\(U1\)P2\)\(U4\)\(\(U2\)\(\(U5\)P4\)\(U1\)P2\)\(U1\)R1\)\n/ FP /^\(\(U5\)\(\(U2\)\(\(U10\)P4\)\(U1\)P4\)\(U5\)_____\(\(U4\)P3\)\(U1\)_______R1\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaduplex-ex AB vienna AA ovrnaduplex IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN FI red.ovrnaduplex FC = 1 FP /^\.\(\.\(\(\(\(\(\.\&\.\)\)\)\)\)\.\)\. 1\,9 : 6\,14 \(-4\.10\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaeval-ex AB vienna AA ovrnaeval IN ../../data/evalrna.fasta IN ../../data/eval1.con IN FI eval.ovrnaeval FC = 2 FP /^GGGGCCCCC\n/ FP /^\(\.\.\.\)\.\.\.\. \( 4\.90\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaeval-test2 AB vienna AA ovrnaeval IN ../../data/evalrna.fasta IN ../../data/eval2.con IN FI eval.ovrnaeval FC = 2 FP /^GGGGCCCCC\n/ FP /^\(\.\.\.\.\)\.\.\. \( 1\.90\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaeval-test3 AB vienna AA ovrnaeval IN ../../data/evalrna.fasta IN ../../data/eval3.con IN FI eval.ovrnaeval FC = 2 FP /^GGGGCCCCC\n/ FP /^\.\.\.\(\.\.\.\.\) \( 4\.90\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaevalpair-ex AB vienna AA ovrnaevalpair IN ../../data/cofold-red.fasta IN ../../data/cofold-red.con IN ../../data/cofold-blue.fasta IN ../../data/cofold-blue.con IN FI red.ovrnaevalpair FC = 2 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\(\(\(\(\.\.\&\.\.\)\)\)\)\(\(\(\.\.\.\.\)\)\)\. \( -4\.40\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnafold-keep AB vienna AA ovrnafold DL keep IN ../../data/rna1.seq IN FI rna1.ssps FC = 154 FP /^%%Pages: 1\n/ FI rna1.ovrnafold FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^\.\(\(\(\.\.\(\(\.\.\.\.\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\.\)\)\)\)\)\.\.\)\)\)\.\. \( -3\.50\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnafold-ex2 AB vienna AA ovrnafold CL -constraintfile ../../data/rna1.fold IN ../../data/rna1.seq IN FI rna1.ssps FC = 153 FP /^%%Pages: 1\n/ FI rna1.ovrnafold FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^\.\.\.\(\(\(\(\.\.\(\(\(\(\(\.\.\.\.\.\)\)\)\)\)\.\.\.\)\)\)\)\.\.\.\.\.\.\.\.\. \( -2\.20\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnafoldpf-ex AB vienna AA ovrnafoldpf CL -temperature 42 IN ../../data/rna2.seq IN FI rna2.ssps FC = 137 FP /%%Pages: 1\n/ FI rna2.ps FC = 178 FP /%%Pages: 1\n/ FI rna2.ps2 FC = 204 FP /%%Pages: 1\n/ FI rna2.ovrnafoldpf FC = 5 FP /\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\.\.\. \( -3\.47\)\n/ FP /\.\.\{\(\,\(\(\(\(\(\.\.\.\.\.\)\)\)\}\}\.\}\}\,\,\.\.\. \[ -4\.45\]\n/ FP / frequency of mfe structure in ensemble 0\.209182; ensemble diversity 6\.08 \n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaheat-ex AB vienna AA ovrnaheat CL -mintemp 30 -maxtemp 120 -step 0.1 -smoothing 4 IN ../../data/cofold-red.fasta IN FI red.ovrnaheat FC = 900 FP /^74\.2\s+0\.00032\d+\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnainverse-ex AB vienna AA ovrnainverse CL -repeats 3 TI 500 IN ../../data/rna3.fold IN ## We can only trust the first result to be the same ## after that random number functions differ on Linux and Tru64 at least FI rna3.ovrnainverse FC = 3 FP 3 /^[ACGU]{76} [0-9][0-9]\n/ FP /^CGGGUUAAAGUUGG.*UAAAGCGUAGCCCGUUAG 30\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnainverse-ex2 AB vienna AA ovrnainverse TI 500 CL -repeats 3 -succeed IN ../../data/rna3.fold IN FI rna3.ovrnainverse FC = 3 FP 3 /^[ACGU]{76} [0-9][0-9]\n/ FP /^CGGGUUAAAGUUGG.*UAAAGCGUAGCCCGUUAG 30\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnalfold-ex AB vienna AA ovrnalfold IN tembl:d00596 IN FI d00596.ovrnalfold FC = 2218 FP /^\.\(\(\(\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\)\.\.\.\(\(\.\.\.\.\)\)\.\.\.\.\.\.\.\)\)\)\. \(-10\.40\) 13193\n/ ##FP /^\.\(\(\(\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\)\.\.\.\(\(\.\.\.\.\)\)\.\.\.\.\.\.\.\)\)\)\. \(-10\.40\) 13193\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnaplot-ex AB vienna AA ovrnaplot IN ../ovrnafold-keep/rna1.ovrnafold IN FI rna1.ovrnaplot FC = 154 FP /%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID ovrnasubopt-ex AB vienna AA ovrnasubopt IN ../../data/rna1.seq IN FI rna1.ovrnasubopt FC = 9 FP /^> rna1 \[100\]\n/ FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA -380 100\n/ FP /^\.\.\.\(\(\(\(\(\.\.\.\.\)\)\.\(\(\(\(\.\(\(\.\.\.\.\.\)\)\)\)\)\)\.\.\.\)\)\)\. -2\.80\n/ FP /^\.\.\.\(\(\(\(\(\.\.\.\.\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\)\)\)\. -3\.80\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ####################################### # VIENNA2 ####################################### ID vrna2dfold-ex AB vienna2 AA vrna2dfold IN ../../data/rnaaln1.seq IN ../../data/rna2d.fold IN FI rna1.vrna2dfold FC = 38 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP 3 /^[.\(\)]+ \( -\d\.\d\d\)/ FP 33 /^\d+\t+\d+\t+[\d -]+\.\d\d\t[.\(\)]+\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaaliduplex-ex AB vienna2 AA vrnaaliduplex IN ../../data/rnaaln1.seq IN ../../data/rnaaln2.seq IN FI rnaaln1.vrnaaliduplex FC = 1 FP /^\.\(\(\(\(\.\.\(\(\(\(\.\&\.\)\)\)\)\.\)\)\)\)\. 27,38 : 14,24 \(-7\.80\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaalifold-ex AB vienna2 AA vrnaalifold IN ../../data/ecoli6s.fasta IN FI ecoli6s.vrnaalifold FC = 2 FP /\(-65\.91 \= -57\.83 \+ -8\.08\) \n/ FP /^\.\.\.\(\(\(\(\(\(\(\(\(\(\(\(\.\(\(\(\.\..*\)\)\.\)\)\)\)\)\)\.\)\.\.\. / FI ecoli6s.ssps FC = 526 FP /^%%Pages: 1\n/ FI ecoli6s.alirnaps FC = 1001 FP /^showpage\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaalifoldpf-ex AB vienna2 AA vrnaalifoldpf IN ../../data/ecoli6s.fasta IN FI ecoli6s.ssps FC = 526 FP /^%%Pages: 1\n/ FI ecoli6s.ps FC = 311 FP /^%%Pages: 1\n/ FI ecoli6s.alirnaps FC = 1001 FP /^showpage\n/ FI ecoli6s.vrnaalifoldpf FC = 156 FP /\(-65\.91 \= -57\.83 \+ -8\.08\) \n/ FP /^AUUUCC[ACGU]+GGGC_CAUGU[ACGU]+GCCCGU_______________CCGAGAAG[ACGU]+CCAA_GGGU[ACGU]+GGCA_UC_UCGGGG_AUUC\n/ FP /^\.\.\.\(\(\(\(\(\(\(\(\(\(\(\{\{\(.*\.\,\..*\)\)\)\)\.\)\.\.\. \[-68\.19\]\n/ FP /^ frequency of mfe structure in ensemble 0\.0247624\n/ FP /^7 sequences; length of alignment 203\n/ FP /^ 64 142 0 100\.0\% 0\.000 CG:1 GC:4 UG:1 UA:1 \n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnacofold-ex AB vienna2 AA vrnacofold ## Example from Algorithms Mol Biol. 2006; 1: 3. ## Partition function and base pairing probabilities of RNA heterodimers ## Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, ## Peter F Stadler and Ivo L Hofacker IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN FI red.vrnacofold FC = 2 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\.\.\.\.\.\.\&\.\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\) \( -4\.70\)\n/ FI red.ssps FC = 230 FP /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnacofoldconc-ex AB vienna2 AA vrnacofoldconc IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN ../../data/cofold-conc.dat IN FI red.vrnacofoldconc FC = 10 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /\.\.\.\.\.\.\.\.\.\.\&\.\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\) \( -4\.70\)\n/ FP /^-5\.332076\t4\.941280\t-15\.286804\t-0\.010157\t-4\.865734\n/ FI red.ssps FC = 230 FP /^%%Pages: 1\n/ FI red.aps FC = 119 FP /^%%Pages: 1\n/ FI red.aaps FC = 156 FP /^%%Pages: 1\n/ FI red.abps FC = 205 FP /^%%Pages: 1\n/ FI red.bps FC = 135 FP /^%%Pages: 1\n/ FI red.bbps FC = 156 FP /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnacofoldpf-ex AB vienna2 AA vrnacofoldpf IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN FI red.vrnacofoldpf FC = 4 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\.\.\.\.\.\.\&\.\(\(\(\(\(\.\.\.\.\.\.\)\)\)\)\) \( -4\.70\)\n/ FP /^\.\,\.\,\(\(\(\{\,\.\&\.\.\,\|\|\|\}\}\}\}\,\.\}\,\,\,\. \[ -5\.57\]\n/ FP /^ frequency of mfe structure in ensemble 0\.242781 , delta G binding\= -0\.46\n/ FI red.ps FC = 203 FP /^%%Pages: 1\n/ FI red.ssps FC = 230 FP /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnadistance-ex AB vienna2 AA vrnadistance CL -distance "f,h" -doalignment IN ../../data/rna4.fold IN FI rna4.vrnadistance FC = 7 FP /^f: 26 \n/ FP /^h: 32 \n/ FP /^\(_____\(\.\(\(\(__\(\(\(\(\.\.\.\.\._____\)\)\)\)_\)\)\)\.\)\)\.\.\.\.\(\(\.\.\(\(\(\(\.\.\.\.\.\)\)\)\)\.\)\)\.\n/ FP /^_\.\.\.\.\.\(_\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\.\.\.\.\)\)\)\)\.\)\)\)_\)_\.\.\.\.__\.__\(\(\(\.\.\.\._\)\)\)_\.___\n/ FP /^\(____\(\(U1\)\(\(U5_\)P7\)\(U1\)P2\)\(U4\)\(\(U2\)\(\(U5\)P4\)\(U1\)P2\)\(U1\)R1\)\n/ FP /^\(\(U5\)\(\(U2\)\(\(U10\)P4\)\(U1\)P4\)\(U5\)_____\(\(U4\)P3\)\(U1\)_______R1\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaduplex-ex AB vienna2 AA vrnaduplex IN ../../data/cofold-red.fasta IN ../../data/cofold-blue.fasta IN FI red.vrnaduplex FC = 1 FP /^\.\(\.\(\(\(\(\(\.\&\.\)\)\)\)\)\.\)\. 1\,9 : 6\,14 \(-4\.10\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaeval-ex AB vienna2 AA vrnaeval IN ../../data/evalrna.fasta IN ../../data/eval1.con IN FI eval.vrnaeval FC = 2 FP /^GGGGCCCCC\n/ FP /^\(\.\.\.\)\.\.\.\. \( 5\.00\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaeval-test2 AB vienna2 AA vrnaeval IN ../../data/evalrna.fasta IN ../../data/eval2.con IN FI eval.vrnaeval FC = 2 FP /^GGGGCCCCC\n/ FP /^\(\.\.\.\.\)\.\.\. \( 3\.70\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaeval-test3 AB vienna2 AA vrnaeval IN ../../data/evalrna.fasta IN ../../data/eval3.con IN FI eval.vrnaeval FC = 2 FP /^GGGGCCCCC\n/ FP /^\.\.\.\(\.\.\.\.\) \( 4\.70\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaevalpair-ex AB vienna2 AA vrnaevalpair IN ../../data/cofold-red.fasta IN ../../data/cofold-red.con IN ../../data/cofold-blue.fasta IN ../../data/cofold-blue.con IN FI red.vrnaevalpair FC = 2 FP /^AUGAAGAUGA\&CUGUCUGUCUUGAGACA\n/ FP /^\.\.\.\.\(\(\(\(\.\.\&\.\.\)\)\)\)\(\(\(\.\.\.\.\)\)\)\. \( -3\.30\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnafold-keep AB vienna2 AA vrnafold DL keep IN ../../data/rna1.seq IN FI rna1.ssps FC = 149 FP /^%%Pages: 1\n/ FI rna1.vrnafold FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\.\. \( -3\.00\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnafold-ex2 AB vienna2 AA vrnafold CL -constraintfile ../../data/rna1.fold IN ../../data/rna1.seq IN FI rna1.ssps FC = 153 FP /^%%Pages: 1\n/ FI rna1.vrnafold FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^\.\.\.\(\(\(\(\.\.\(\(\(\(\(\.\.\.\.\.\)\)\)\)\)\.\.\.\)\)\)\)\.\.\.\.\.\.\.\.\. \( -1\.80\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnafoldpf-ex AB vienna2 AA vrnafoldpf CL -temperature 42 IN ../../data/rna2.seq IN FI rna2.ssps FC = 140 FP /%%Pages: 1\n/ FI rna2.ps FC = 176 FP /%%Pages: 1\n/ FI rna2.ps2 FC = 200 FP /%%Pages: 1\n/ FI rna2.vrnafoldpf FC = 5 FP /^\.\.\(\(\(\(\(\.\.\(\(\(\.\.\.\)\)\)\.\.\)\)\)\)\)\.\.\. \( -3\.82\)\n/ FP /^\.\.\(\(\(\(\(\{\{\(\,\.\.\.\.\)\)\)\,\.\}\)\)\)\}\.\.\. \[ -4\.85\]\n/ FP / frequency of mfe structure in ensemble 0\.193301; ensemble diversity 6\.05 \n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaheat-ex AB vienna2 AA vrnaheat CL -mintemp 30 -maxtemp 120 -step 0.1 -smoothing 4 IN ../../data/cofold-red.fasta IN FI red.vrnaheat FC = 900 FP /^74\.2\s+0\.001140\d+\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnainverse-ex AB vienna2 AA vrnainverse CL -repeats 3 TI 500 IN ../../data/rna3.fold IN ## We can only trust the first result to be the same ## after that random number functions differ on Linux and Tru64 at least FI rna3.vrnainverse FC = 3 FP 3 /^[ACGU]{76} [0-9][0-9]\n/ FP /^CGGGUUAACGGUUA[ACGU]+GUAGGGUAGCCCGUAAU 27\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnalalifoldpf-ex AB vienna2 AA vrnalalifoldpf IN ../../data/ecoli6s.fasta IN FI ecoli6s.vrnalalifoldpf FC = 3 FP 2 /^\n/ FP /^[ACGU]+GGGC_CAUGU[ACGU]+CCGU_______________CCG[ACGU]+CCAA_GGGU[ACGU]+GGCA_UC_UCGGGG_AUUC\n/ FI ecoli6s.alirna FC = 3 FP /^7 sequence; length of alignment 203\n/ FP /^alifold output\n/ FP 1 /^\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnalfold-ex AB vienna2 AA vrnalfold IN tembl:d00596 IN FI d00596.vrnalfold FC = 235 FP /^\.\(\(\(\(\(\(\.\.\(\(\(\(\(\(\(\(\.\(\(\(\(\(\.\.\.\.\.\.\.\)\)\)\)\)\.\)\)\)\.\)\)\)\)\)\.\.\.\)\)\)\)\)\)\. \(-17\.10\) 15120 z\= -3\.768\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnalfold-zdata AB vienna2 AA vrnalfold IN ../../data/rna1.seq IN FI rna1.vrnalfold FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^ \( -3\.00\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnalfoldz-ex AB vienna2 AA vrnalfoldz IN ../../data/rna1.seq IN FI rna1.vrnalfoldz FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^ \( -3\.00\)\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnapkplex-ex AB vienna2 AA vrnapkplex IN ../../data/rna1.seq IN FI rna1.vrnapkplex FC = 2 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA\n/ FP /^\.\.\.\.\.\.\.\.\.\.\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\.\. \(5\.10\)\n/ FI rna1.ssps FC = 149 FP /^showpage\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaplfold-ex AB vienna2 AA vrnaplfold IN ../../data/rna1.seq IN FI rna1.vrnaplfold FC = 42 FP / [\#]i[\$]\t.*\t31\t$\n/ FI rna1.plex FC = 41 FP 38 /^\d+\t\d+\t\d+\t\d+\t\n/ FP 1 /^\d+\t\d+\t\-0\t\d+\t\n/ FP 1 /^\d+\t\d+\t\d+\t\-0\t\n/ FI rna1.ssps FC = 219 FP 1 /^%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnaplot-ex AB vienna2 AA vrnaplot IN ../vrnafold-keep/rna1.vrnafold IN FI rna1.vrnaplot FC = 149 FP /%%Pages: 1\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ID vrnasubopt-ex AB vienna2 AA vrnasubopt IN ../../data/rna1.seq IN FI rna1.vrnasubopt FC = 4 FP /^CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA -300 100\n/ FP /^\.\.\.\.\.\.\(\(\.\.\.\.\)\)\.\(\(\(\(\(\.\.\.\.\.\.\.\.\)\)\)\)\)\.\.\.\.\.\.\. -2\.20\n/ FP /^\(\(\(\(\.\.\.\.\.\(\(\(\(\(\.\.\.\.\.\)\)\)\)\)\.\.\.\)\)\)\)\.\.\.\.\.\.\.\.\. -2\.70\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 0 // ############################################################### # # MIRA fragment assembly # Needs to be installed, use MIRA local copy of demo data # ############################################################### ID emira-ex AB mira AA emira TI 300 PP ln -f -s /homes/pmr/src/mira-2.8.3/minidemo/data/bbdataset1/cjejuni_demo* . PP EMBOSS_MIRA=mira283/mira PP export EMBOSS_MIRA CL -setparam fasta -project cjejuni_demo -grade accurate CL -mxti -rns tigr -orh QQ rm cjejuni_demo_backbone_in.gbf QQ rm cjejuni_demo_in.fasta QQ rm cjejuni_demo_in.fasta.qual QQ rm cjejuni_demo_straindata_in.txt QQ rm cjejuni_demo_traceinfo_in.xml FI EdIt.log FC =0 DI cjejuni_demo_info DI cjejuni_demo_log DI cjejuni_demo_results FI stderr FC = 1 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2413 FP 4 /^Contig id: 13\n/ FP 5 /^Contig id: 2\n/ // ID emiraest-ex AB mira AA emiraest CL -setparam fasta TI 300 IN ## Input files absolutely require the step1 prefix for MIRA up to 2.8.3 PP EMBOSS_MIRAEST=mira283/miraEST PP export EMBOSS_MIRAEST PP uncover_at /homes/pmr/src/mira-2.8.3/minidemo/data/fasta_estset1/triphysaria_versicolor.masked.fasta -P "-CL:mbc=on:mbcmeg=240" -n -a -r /homes/pmr/src/mira-2.8.3/minidemo/data/fasta_estset1/triphysaria_versicolor.fasta step1_in.fasta >ttt PP rm ttt PP ln -f -s /homes/pmr/src/mira-2.8.3/minidemo/data/fasta_estset1/triphysaria_versicolor.fasta.qual step1_in.fasta.qual PP touch step1_straindata_in.txt QQ rm step1_in.fasta.qual QQ rm step1_straindata_in.txt FI EdIt.log FC =0 DI step1_info DI step1_log DI step1_results FI step1_in.fasta FC = 43967 FP 2396 /^>/ FI step1_nosnps_remain.caf FC = 107852 FP 1595 /^BaseQuality : / FI step1_snpsinSTRAIN_default.caf FC = 47668 FP 801 /^BaseQuality : / FI step1_res_cafstrainnames.txt FC = 2 FP /^step1_snpsinSTRAIN_default.caf\tdefault\n/ FP /^step1_nosnps_remain.caf\tremain\n/ FI step2_reads.caf FC = 50955 FP 1426 /^BaseQuality : / FI step2_straindata.txt FC = 1429 FP 309 /^default_c\d+\tdefault\n/ DI default_info DI default_log DI default_results DI remain_info DI remain_log DI remain_results DI step3_info DI step3_log DI step3_results FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FP 3 /Error while trying to load parameter file me_step[1-9]\.par/ FI stdout FC = 123640 FP 4 /^Contig id: 138\n/ FP 2 /^Contig id: 1380\n/ FP 1 /^Contig id: 1390\n/ // ############################################################### # # CBS TOOLS # Need to be installed individually # ############################################################### ID echlorop-ex AB cbstools AA echlorop RQ chlorop IN ../../data/cbs/test1.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test1.echlorop FC = 10 FP /^P48786; 1088 0\.434 - -0\.663 28\n/ // ID echlorop-full AB cbstools AA echlorop RQ chlorop CL -full IN ../../data/cbs/test1.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test1.echlorop FC = 1106 FP /^P48786; 1088 0\.434 - -0\.663 28\n/ FP /^ 29 Q 0\.144 0\.008 -0\.663\n/ // ID echlorop-ex2 AB cbstools AA echlorop RQ chlorop IN ../../data/cbs/test12.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test12.echlorop FC = 21 FP /^P48786; 1088 0\.434 - -0\.663 28\n/ // ID echlorop-full2 AB cbstools AA echlorop RQ chlorop CL -full IN ../../data/cbs/test12.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test12.echlorop FC = 4188 FP /^P48786; 1088 0\.434 - -0\.663 28\n/ FP /^ 29 Q 0\.144 0\.008 -0\.663\n/ // ID elipop-ex AB cbstools AA elipop RQ lipop IN ../../data/cbs/5h2a_crigr.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 5h2a_crigr.elipop FC = 5 FP /5H2A_CRIGR LipoP1\.0 SEQUENCE 1 70 0 \+ \. \#you can have comments after the ID\n/ FP /^5H2A_CRIGR LipoP1\.0:Signal CYT 1 1 -0\.200913 \+ 0 \#M\n/ // ID enetnglyc-ex AB cbstools AA enetnglyc RQ netNglyc IN ../../data/cbs/LEUK_RAT.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI leuk_rat.enetnglyc FC = 40 FP / Warning: This sequence may not contain a signal peptide\!\!/ FP /^ LEUK_RAT 0\.112 32 N 0\.088 16 N 0\.362 8 N 0\.119 N 0\.104 N\n/ FP /^LEUK_RAT 274 NGTV 0\.7323 \(9\/9\) \+\+\n/ FP /^LEUK_RAT 300 NKSS 0\.5404 \(6\/9\) \+\n/ // ID enetoglyc-ex AB cbstools AA enetoglyc RQ netOglyc IN ../../data/cbs/LEUK_RAT.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI leuk_rat.enetoglyc FC = 129 FP 45 /^LEUK_RAT\s+T\s+.*\s+T\s+/ FP 8 /^LEUK_RAT\s+T\s+.*\s+\.\s+/ FP 35 /^LEUK_RAT\s+S\s+.*\s+S\s+/ FP 24 /^LEUK_RAT\s+S\s+.*\s+\.\s+/ FP 112 /^LEUK_RAT\s+/ FP /LEUK_RAT S 25 0\.502 0\.029 S -\n/ // ID enetphos-ex AB cbstools AA enetphos IN ../../data/cbs/EFTU_HUMAN.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eftu_human.enetphos FC = 748 FP /^# EFTU_HUMAN 5 T MAAATLLRA 0.776 PKC YES\n/ // ID eprop-ex AB cbstools AA eprop RQ prop IN ../../data/cbs/EDA_HUMAN.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI eda_human.eprop FC = 73 FP /EDA_HUMAN 8 GYPEVER\|RE 0\.057 \.\n/ // ID esignalp-ex AB cbstools RQ signalp AA esignalp IN ../../data/cbs/test.seq IN IN IN IN IN IN FI stderr FC = 24 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI test.esignalp FC = 168 FP /trained on eukaryotes/ FP /^\# Measure Position Value Cutoff signal peptide\?\n/ FP /^ max\. C 26 0\.681 0\.32 YES\n/ FP /^ max\. Y 26 0\.731 0\.33 YES\n/ FP /^ max\. S 18 0\.982 0\.87 YES\n/ FP /^ mean S 1-25 0\.832 0\.48 YES\n/ FP /^ D 1-25 0\.782 0\.43 YES\n/ FP /^\# Most likely cleavage site between pos. 25 and 26: VSS-TE\n/ // ID etmhmm-ex AB cbstools AA etmhmm RQ tmhmm IN ../../data/cbs/5h2a_crigr.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI 5h2a_crigr.etmhmm FC = 20 FP /^# 5H2A_CRIGR Length: 471\n/ FP /^# 5H2A_CRIGR Number of predicted TMHs: 7\n/ FP /^# 5H2A_CRIGR Exp number of AAs in TMHs: 159\.47336\n/ FP /^# 5H2A_CRIGR Exp number, first 60 AAs: 0\.01677\n/ FP /^# 5H2A_CRIGR Total prob of N-in: 0\.00629\n/ FP /^5H2A_CRIGR TMHMM2\.0 outside 1 76\n/ FP /^5H2A_CRIGR TMHMM2\.0 TMhelix 77 99\n/ // ID eyinoyang-ex AB cbstools AA eyinoyang RQ yinoyang IN ../../data/cbs/CBG_HUMAN.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI cbg_human.eyinoyang FC = 39 FP /^ CBG_HUMAN 0\.645 23 Y 0\.717 23 Y 0\.981 13 Y 0\.886 Y 0\.801 Y\n/ // ID eyinoyang-ex2 AB cbstools AA eyinoyang RQ yinoyang IN ../../data/cbs/LEUK_RAT.fsa IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI leuk_rat.eyinoyang FC = 74 FP /^LEUK_RAT 6 S \+\+ 0\.5334 0\.4196 0\.5159\n/ // ####################################### # CLUSTALOMEGA ####################################### ID eomega-ex AB clustalomega AA eomega CL ../../data/globins.fasta IN FI globins.aln FC = 28 FP /^>HBA_HORSE Sw:Hba_Horse => HBA_HORSE\n/ FP /^---------VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDL---\n/ FP /^---SHGSAQVKAHGKKVGDALTLAVGHLDDLP--G---ALSNLSDLHAHKLRVDPVNFKL\n/ FP /^LSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR------\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eomegapp-ex AB clustalomega AA eomegapp CL ../../data/op1.ali ../../data/op2.ali IN FI op1.aln FC = 224 FP /^>OPSD_CRIGR P28681 Rhodopsin\n/ FP /^-----------------MNGTEGPNFYV-------PFSNATGVVRSPFEYP-----QYYL\n/ FP /^AEPWQFSMLAAYMFLLIVLGFP---INFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVF\n/ FP /^GGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVICKPMSNFRF\n/ FP /^GENHAIMGVVFTWIMALACAAPPLVGWSRYIPEGMQCSCGVDYYTLKPEVNNESF-VIYM\n/ FP /^FVVHFTIPLIVIFFCYGQLVFTVKEAAAQQQ-------------ESATTQKAEKEVTRMV\n/ FP /^ILMVVFFLICWFPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFR\n/ FP /^NCMLT---TLCCGKNILGDDEAS---ATASKT---ETSQVAPA-\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eomegash-ex AB clustalomega AA eomegash CL ../../data/twoglob.fasta ../../data/globins4.hmm IN FI twoglob.aln FC = 8 FP /^>HBA_HUMAN/ FP /^MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\n/ FP /^KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\n/ FP /^AVHASLDKFLASVSTVLTSKYR\n/ FP /^>HBA_BOVFRAG/ FP /^------DKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\n/ FP /^AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP\n/ FP /^AVHASLDKFLANVST-------\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ID eomegasp-ex AB clustalomega AA eomegasp CL ../../data/ops.fasta ../../data/op1.ali IN FI ops.aln FC = 112 FP /^>OPSD_CALPD Q6W3E1 Rhodopsin\n/ FP /^-MNGTEGPNFYV--------PFSNKTGVVRSPFEEP-----QYYLAEPWQFSCLAAYMFM\n/ FP /^LIVLGFP---INFLTLYVTIQHKKLRTPLNYILLNLAIADLFMVFGGFTTTLYTSLHGYF\n/ FP /^VFGPTGCDLEGFFATLGGEIALWSLVVLAIERYIVVCKPMSNFRFGENHAIMGVAFTWVM\n/ FP /^ALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMVVIFFCY\n/ FP /^GQLVFTVKEAAAQQ--QE-------------SATTQKAEKEVTRMVIIMVIAFLICWLPY\n/ FP /^AGVAFYIFTHQGSNFGPILMTLPAFFAKTSAVYNPVIYIMLNKQFRTCMLT---TLCCGK\n/ FP /^IPLGDDEASATAS-KTET-----SQVAPA\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / // ############################################################### # # IPRSCAN # iprscan needs to be installed separately # ############################################################### ID eiprscan-ex AB iprscan AA eiprscan RQ iprscan TI 1500 QQ ../../../scripts/eiprscan-sort.pl iprtest.eiprscan CL -nocrc -goterms -iprlookup IN ../../data/iprtest.seq IN IN raw IN FI stderr FC = 26 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI iprtest.eiprscan FC = 46 FP 20 /^Q9RHD9/ FP 6 /^RS16_ECOLI/ FP 20 /^Y902_MYCTU/ // #################################################### # # multifield queries with query operators # #################################################### ID qsyn-idlist AP seqret CL "tsw-{id:hba_human | id:hbb_human}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 1 /^>HBB_HUMAN/ FP 2 /^>/ // ID qsyn-idlist2 AP seqret CL "tsw{hba_human, hbb_human}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 1 /^>HBB_HUMAN/ FP 2 /^>/ // ID qsyn-idlist3 AP seqret CL "tsw{hba_human|hbb_human}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 2 /^>/ // ID qsyn-idlist4 AP seqret CL "tsw-id{hba_human|hbb_human}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 2 /^>/ // ID qsyn-idlist-mix1 AP seqret CL "tsw{HBA_HUMAN, P68871}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 1 /^>HBB_HUMAN/ FP 2 /^>/ // ID qsyn-idlist-mix2 AP seqret CL "tsw{P68871, HBA_HUMAN}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 1 /^>HBB_HUMAN/ FP 2 /^>/ // ID qsyn-idlist-mix3 AP seqret CL "tsw{P68871, ABCDEF, HBA_HUMAN}" stdout -auto FI stdout FP 0 /^>HIRA_TAKRU/ FP 1 /^>HBA_HUMAN/ FP 1 /^>HBB_HUMAN/ FP 2 /^>/ // ID qsyn-id-not AP seqret CL "tsw-{id:h* ! des:Hemoglobin}" stdout -auto FI stdout FP /^>HIRA_TAKRU/ FP 0 /^>HBA_HUMAN/ FP 2 /^>/ // ID qsyn-id-not-nospace AP seqret CL "tsw-{id:h*!des:Hemoglobin}" stdout -auto FI stdout FP /^>HIRA_TAKRU/ FP 0 /^>HBA_HUMAN/ FP 2 /^>/ // ID qsyn-id2-not AP seqret CL "qanxflatall-{id:m1190* ! des:1a}" stdout -auto FI stdout FP /^>M11905/ FP 0 /^>M11903/ FP 2 /^>/ // ID qsyn-acc-not AP seqret CL "qanxflatall-{acc:x01958 ! des:1a}" stdout -auto FI stdout FP /^>M11905/ FP 0 /^>M11903/ FP 2 /^>/ // ID qsyn-part1 AP ontoget CL "edam-{des:cdna}" stdout -auto FI stdout FP 1 /def: .*cDNA or mRNA/ FP 3 /^id: / // ID qsyn-part2 AP ontoget CL "edam-{des:mrna}" stdout -auto FI stdout FP 1 /def: .*cDNA or mRNA/ FP 8 /^id: / // ID qsyn-and AP ontoget CL "edam-{des:cdna & des:mrna}" stdout -auto FI stdout FP 1 /def: .*cDNA or mRNA/ FP 2 /^id: / // ID qsyn-eor AP ontoget CL "edam-{des:cdna ^ des:mrna}" stdout -auto FI stdout FP 0 /def: .*cDNA or mRNA/ FP 1 /def: .*cDNA/ FP 6 /def: .*mRNA/ FP 7 /^id: / // ID qsyn-not AP ontoget CL "edam-{nam:rna ! des:sequence}" stdout -auto FI stdout FP 0 /def:.*sequence / FP 4 /def:.*sequences/ FP 24 /^id: / // #################################################### # # query syntax operators by access method # #################################################### ID qacc-or-emboss AP seqret CL "qanxflat-id{m11903 | m11904 | m11905}" stdout -auto FI stdout FP 3 /^>/ FP 3 /^>M1190/ // ID qacc-and-emboss AP seqret CL "qanxflat-acc{x01958 & m11905}" stdout -auto FI stdout FP 1 /^>/ FP 1 /^>M11905/ // ID qacc-eor-emboss AP seqret CL "qanxflat-acc{x01958 ^ m11905}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>M11905/ FP 1 /^>M11903/ FP 1 /^>M11904/ // ID qacc-not-emboss AP seqret CL "qanxflat-acc{x01958 ! m11905}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>M11905/ FP 1 /^>M11903/ FP 1 /^>M11904/ // ID qacc-or-emblcd AP seqret CL "qanflat-id{m11903 | m11904 | m11905}" stdout -auto FI stdout FP 3 /^>/ FP 3 /^>M1190/ // ID qacc-and-emblcd AP seqret CL "qanflat-acc{x01958 & m11905}" stdout -auto FI stdout FP 1 /^>/ FP 1 /^>M11905/ // ID qacc-eor-emblcd AP seqret CL "qanflat-acc{x01958 ^ m11905}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>M11905/ FP 1 /^>M11903/ FP 1 /^>M11904/ // ID qacc-not-emblcd AP seqret CL "qanflat-acc{x01958 ! m11905}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>M11905/ FP 1 /^>M11903/ FP 1 /^>M11904/ // ID qacc-or-embossgcg AP seqret CL "qanxgcg-id{v00294 | v00295 | v00296}" stdout -auto FI stdout FP 3 /^>/ FP 3 /^>V0029/ // ID qacc-and-embossgcg AP seqret CL "qanxgcg-acc{v0029* & v00295}" stdout -auto FI stdout FP 1 /^>/ FP 1 /^>V00295/ // ID qacc-eor-embossgcg AP seqret CL "qanxgcg-acc{v0029* ^ v00295}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>V00295/ FP 1 /^>V00294/ FP 1 /^>V00296/ // ID qacc-not-embossgcg AP seqret CL "qanxgcg-acc{v0029* ! v00295}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>V00295/ FP 1 /^>V00294/ FP 1 /^>V00296/ // ID qacc-or-gcg AP seqret CL "qangcg-id{v00294 | v00295 | v00296}" stdout -auto FI stdout FP 3 /^>/ FP 3 /^>V0029/ // ID qacc-and-gcg AP seqret CL "qangcg-acc{v0029* & v00295}" stdout -auto FI stdout FP 1 /^>/ FP 1 /^>V00295/ // ID qacc-eor-gcg AP seqret CL "qangcg-acc{v0029* ^ v00295}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>V00295/ FP 1 /^>V00294/ FP 1 /^>V00296/ // ID qacc-not-gcg AP seqret CL "qangcg-acc{v0029* ! v00295}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>V00295/ FP 1 /^>V00294/ FP 1 /^>V00296/ // ID qacc-or-srswww AP seqret CL "srs:embl-id{m11903 | m11904 | m11905}" stdout -auto FI stdout FP 3 /^>/ FP 3 /^>M1190/ // ID qacc-and-srswww AP seqret CL "srs:embl-acc{x01958 & m11905}" stdout -auto FI stdout FP 1 /^>/ FP 1 /^>M11905/ // ID qacc-eor-srswww-fail ER 1 AP seqret CL "srs:embl-acc{x01958 ^ m11905}" stdout -auto FI stderr FP 0 /Warning: / FP 2 /Error: / FP 1 /Died: / FP /^Error: Query link operator '\^' not supported by access method 'srswww'/ // ID qacc-not-srswww AP seqret CL "srs:embl-acc{x01958 ! m11905}" stdout -auto FI stdout FP 2 /^>/ FP 0 /^>M11905/ FP 1 /^>M11903/ FP 1 /^>M11904/ // #################################################### # # chado access method for gmod.org chado schemas # #################################################### ID chado-genedb-chromosome RQ postgresql AP featcopy CL tgenedb:'NCLIV_chrIb' -auto FI ncliv_chrib.gff FP 2285 /^NCLIV_chrIb/ ## sequence-region range: 1 1908326 FP 1 /^##sequence-region NCLIV_chrIb/ // ID chado-genedb-gene RQ postgresql AP featcopy CL tgenedb:'LinJ.18.0820' stdout -auto FI stdout FP 4 /^LinJ.18/ ## sequence-region range: 329420 337405 FP 1 /^##sequence-region LinJ.18/ // ID chado-flybase-transcript RQ postgresql AP featcopy CL tflybase:'FBtr0076663' -auto FI 3l.gff FP 921 /^3L/ ## sequence-region range: 8400369 8404675 FP 1 /^##sequence-region 3L/ FI stderr FC < 5 // ID chado-flybase-gene RQ postgresql AP featcopy CL tflybase:'FBgn0030105' FBgn0030105.gff -auto FI FBgn0030105.gff FP 183 /^X/ ## sequence-region range: 9110926 9111401 FP 1 /^##sequence-region X/ FP 1 /9110926.9110958.*five_prime_UTR_FBgn0030105.*FBtr0071309.*parent_type=mRNA/ FP 1 /CDS.*9110959.9111128.*ID=CDS_FBgn0030105.*Parent=FBtr0071309;/ FP 1 /intron.*9111129.9111181.*;Name=CG15369-in;Parent=FBtr0071309;/ //