codcopy Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Copy and reformat a codon usage table Description codcopy reads and writes a codon usage table. Rather than a copy utility, it is intended as a format conversion utility so that codon usage data can be exported to other applications that support only a single format. This program supports all available codon usage input and output formats. Usage Here is a sample session with codcopy % codcopy Copy and reformat a codon usage table Codon usage file: Eecoli.cut Codon usage output file [eecoli.cut]: Go to the output files for this example Command line arguments Copy and reformat a codon usage table Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-infile] codon Codon usage table name [-outfile] outcodon Codon usage table name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-infile" associated qualifiers -format1 string Data format "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 string Output format specific to this data type General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format codcopy reads a codon usage file. Output file format codcopy writes a codon usage table. The user can choose any supported output format. ,p> See the full specification of codon tabel formats at: http://emboss.sourceforge.net/docs/themes/CodonUsage.html Output files for usage example File: eecoli.cut #Species: Escherichia coli K12 #Division: gbbct #Release: CUTG146 #CdsCount: 5045 #Coding GC 51.81% #1st letter GC 58.93% #2nd letter GC 40.69% #3rd letter GC 55.80% #Codon AA Fraction Frequency Number GCA A 0.214 20.299 32456 GCC A 0.269 25.493 40761 GCG A 0.355 33.631 53773 GCT A 0.162 15.354 24549 TGC C 0.554 6.431 10283 TGT C 0.446 5.180 8282 GAC D 0.372 19.047 30454 GAT D 0.628 32.219 51514 GAA E 0.690 39.570 63268 GAG E 0.310 17.782 28431 TTC F 0.425 16.580 26510 TTT F 0.575 22.423 35852 GGA G 0.108 7.925 12671 GGC G 0.402 29.403 47013 GGG G 0.150 10.994 17578 GGT G 0.340 24.838 39714 CAC H 0.429 9.712 15529 CAT H 0.571 12.903 20630 ATA I 0.072 4.290 6860 ATC I 0.419 24.999 39971 ATT I 0.510 30.427 48649 AAA K 0.767 33.618 53752 AAG K 0.233 10.198 16305 CTA L 0.036 3.860 6172 CTC L 0.104 11.045 17660 CTG L 0.496 52.821 84455 CTT L 0.104 11.051 17670 TTA L 0.131 13.913 22246 TTG L 0.129 13.727 21948 ATG M 1.000 27.778 44414 AAC N 0.551 21.611 34554 AAT N 0.449 17.633 28193 CCA P 0.192 8.524 13629 CCC P 0.125 5.531 8843 CCG P 0.524 23.235 37150 CCT P 0.159 7.045 11265 CAA Q 0.349 15.474 24742 CAG Q 0.651 28.832 46100 AGA R 0.037 2.056 3287 AGG R 0.022 1.216 1944 CGA R 0.064 3.542 5663 CGC R 0.398 22.005 35184 CGG R 0.098 5.391 8619 CGT R 0.381 21.020 33609 AGC S 0.277 16.031 25632 AGT S 0.151 8.723 13947 TCA S 0.123 7.137 11411 TCC S 0.148 8.591 13736 TCG S 0.154 8.916 14256 TCT S 0.147 8.507 13601 ACA T 0.131 7.035 11248 ACC T 0.435 23.362 37354 ACG T 0.268 14.371 22977 ACT T 0.166 8.922 14265 GTA V 0.154 10.883 17400 GTC V 0.215 15.221 24336 GTG V 0.371 26.253 41976 GTT V 0.260 18.394 29410 TGG W 1.000 15.303 24468 TAC Y 0.429 12.243 19576 TAT Y 0.571 16.326 26103 TAA * 0.642 2.025 3237 TAG * 0.072 0.228 365 TGA * 0.286 0.902 1443 Data files None Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description aligncopy Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections cai Calculate codon adaptation index chips Calculates Nc codon usage statistic codcmp Codon usage table comparison cusp Create a codon usage table from nucleotide sequence(s) cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence featcopy Reads and writes a feature table featreport Reads and writes a feature table feattext Return a feature table original text listor Write a list file of the logical OR of two sets of sequences makenucseq Create random nucleotide sequences makeprotseq Create random protein sequences maskambignuc Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features maskseq Write a sequence with masked regions newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequences nthseqset Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) sequences, skipping first few splitsource Split sequence(s) into original source sequences splitter Split sequence(s) into smaller sequences syco Draw synonymous codon usage statistic plot for a nucleotide sequence trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file union Concatenate multiple sequences into a single sequence vectorstrip Removes vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None