nthseqset 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 Reads and writes (returns) one set of sequences from many Description nthseqset writes to file a single sequence alignment (set) from an input stream of sequence sets. The sequence set is specified by number, which is the order it appears in the input file. The output file name may be specified. Usage Here is a sample session with nthseqset % nthseqset -osf phylip Reads and writes (returns) one set of sequences from many Input sequence set(s): globins-all.phy The number of the sequence set to output [1]: 2 output sequence(s) [globins-all.phylip]: Go to the input files for this example Go to the output files for this example Command line arguments Reads and writes (returns) one set of sequences from many Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqsetall Sequence set(s) filename and optional format, or reference (input USA) -number integer [1] The number of the sequence set to output (Integer 1 or more) [-outseq] seqoutall [.] Sequence set(s) filename and optional format (output USA) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -feature boolean Use feature information Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 string Output directory 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 nthseqset reads one or more nucleotiode or protein sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example File: globins-all.phy 7 164 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN-VD EVGGEALGR- LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN-EE EVGGEALGR- LLVVYPWTQR HBA_HUMAN ---------- ----VLSPAD KTNVKAA-WG KVGAHAGEYG AEALERMFLS HBA_HORSE ---------- ----VLSAAD KTNVKAA-WS KVGGHAGEYG AEALERMFLG MYG_PHYCA -------VLS EGEWQLVLHV WAKVEAD-VA GHGQDILIR- LFKSHPETLE GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN LKGTFAALSE FPTTKTYFPH FDLSHGSAQV KGHGKKVADA LTNAVAHVDD MPNALSALSD FPTTKTYFPH FDLSHGSAQV KAHGKKVGDA LTLAVGHLDD LPGALSNLSD KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD LFSFLKGTSE VPQNNPELQA HAGKVFKLVY EAAIQLQVTG VVVTDATLKN LHCDKLH--V DPENFRLLGN VLVCVLAHHF GKEFTPPVQA AYQKVVAGVA LHCDKLH--V DPENFRLLGN VLVVVLARHF GKDFTPELQA SYQKVVAGVA LHAHKLR--V DPVNFKLLSH CLLVTLAAHL PAEFTPAVHA SLDKFLASVS LHAHKLR--V DPVNFKLLSH CLLSTLAVHL PNDFTPAVHA SLDKFLSSVS SHATKHK--I PIKYLEFISE AIIHVLHSRH PGDFGADAQG AMNKALELFR LSGKHAK--S FQVDPQYFKV LAAVIADTVA AGDAGFEKLM SMICILLRSA LGSVHVSKGV ADAHFPVVKE AILKTIKEVV GAKWSEELNS AWTIAYDELA NALAHKYH-- ---- NALAHKYH-- ---- TVLTSKYR-- ---- TVLTSKYR-- ---- KDIAAKYKEL GYQG Y--------- ---- IVIKKEMNDA A--- 7 167 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN--V DEVGGEALGR LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN--E EEVGGEALGR LLVVYPWTQR HBA_HUMAN ---------V LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT HBA_HORSE ---------V LSAADKTNVK AAWSKVGGHA GEYGAEALER MFLGFPTTKT GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE MYG_PHYCA ---------V LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN -----LKGTF YFPHF-DLS- ----HGSAQV KGHGKKVADA LTNAVAHVDD -----MPNAL YFPHF-DLS- ----HGSAQV KAHGKKVGDA LTLAVGHLDD -----LPGAL FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD T--EKMSMKL KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH -----HEAEL LFSFLKGTSE VP--QNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL ATLSELHCDK LHVDPENFRL LGNVLVCVLA HHFGKEFTPP VQAAYQKVVA AALSELHCDK LHVDPENFRL LGNVLVVVLA RHFGKDFTPE LQASYQKVVA SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA VHASLDKFLS RDLSGKHAKS FQVDPQYFKV LAAVIADTVA AG-------- -DAGFEKLMS KPLAQSHATK HKIPIKYLEF ISEAIIHVLH SRHPGDFGAD AQGAMNKALE KNLGSVHVSK G-VADAHFPV VKEAILKTIK EVVGAKWSEE LNSAWTIAYD GVANALAHKY H------ GVANALAHKY H------ SVSTVLTSKY R------ SVSTVLTSKY R------ MICILLRSAY ------- LFRKDIAAKY KELGYQG ELAIVIKKEM NDAA--- Output file format The output is a standard EMBOSS sequence file. The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. The output is the specified ordinal sequence set from the input USA. In the example, the second sequence set from the input file will be written out to the specified output file. Output files for usage example File: globins-all.phylip 7 167 HBB_HUMAN --------VH LTPEEKSAVT ALWGKVN--V DEVGGEALGR LLVVYPWTQR HBB_HORSE --------VQ LSGEEKAAVL ALWDKVN--E EEVGGEALGR LLVVYPWTQR HBA_HUMAN ---------V LSPADKTNVK AAWGKVGAHA GEYGAEALER MFLSFPTTKT HBA_HORSE ---------V LSAADKTNVK AAWSKVGGHA GEYGAEALER MFLGFPTTKT GLB5_PETMAPIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE MYG_PHYCA ---------V LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE LGB2_LUPLU--------GA LTESQAALVK SSWEEFNANI PKHTHRFFIL VLEIAPAAKD FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN -----LKGTF FFDSFGDLSN PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN -----LKGTF YFPHF-DLS- ----HGSAQV KGHGKKVADA LTNAVAHVDD -----MPNAL YFPHF-DLS- ----HGSAQV KAHGKKVGDA LTLAVGHLDD -----LPGAL FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD T--EKMSMKL KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH -----HEAEL LFSFLKGTSE VP--QNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL ATLSELHCDK LHVDPENFRL LGNVLVCVLA HHFGKEFTPP VQAAYQKVVA AALSELHCDK LHVDPENFRL LGNVLVVVLA RHFGKDFTPE LQASYQKVVA SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SNLSDLHAHK LRVDPVNFKL LSHCLLSTLA VHLPNDFTPA VHASLDKFLS RDLSGKHAKS FQVDPQYFKV LAAVIADTVA AG-------- -DAGFEKLMS KPLAQSHATK HKIPIKYLEF ISEAIIHVLH SRHPGDFGAD AQGAMNKALE KNLGSVHVSK G-VADAHFPV VKEAILKTIK EVVGAKWSEE LNSAWTIAYD GVANALAHKY H------ GVANALAHKY H------ SVSTVLTSKY R------ SVSTVLTSKY R------ MICILLRSAY ------- LFRKDIAAKY KELGYQG ELAIVIKKEM NDAA--- Data files None. Notes In EMBOSS, when an application has to write out many sequences, they are typically all written to a single file. This default behaviour can be changed by using the qualifier -ossingle which forces each sequence to be written to its own file. The program seqretsplit will take a file containing many sequences and will output many files, each containing one sequence. However you have no choice over the naming of the files - they are named after the ID name fo the sequence they contain. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with a status of 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 codcopy Copy and reformat a codon usage table 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 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 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