                                  nthseqset



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Function

   Read and write (return) 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
Read and write (return) 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

Read and write (return) one set of sequences from many
Version: EMBOSS:6.6.0.0

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve 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         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write 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     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask 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         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) 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      Remove 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
