                                   notseq



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Function

   Write to file a subset of an input stream of sequences

Description

   notseq writes to file a subset of an input stream of sequences. The
   list of sequence names or accession numbers to exclude from output is
   provided as a string. Optionally, the excluded sequences are also
   written to file.

Usage

   Here is a sample session with notseq

   In this case the excluded sequences (myg_phyca and lgb2_luplu) are not
   saved to any file:


% notseq
Write to file a subset of an input stream of sequences
Input (gapped) sequence(s): globins.fasta
Sequence names to exclude: myg_phyca,lgb2_luplu
output sequence(s) [hbb_human.fasta]: mydata.seq


   Go to the input files for this example
   Go to the output files for this example

   Example 2

   Here is an example where the sequences to be excluded are saved to
   another file:


% notseq -junkout hb.seq
Write to file a subset of an input stream of sequences
Input (gapped) sequence(s): globins.fasta
Sequence names to exclude: hb*
output sequence(s) [hbb_human.fasta]: mydata.seq


   Go to the output files for this example

Command line arguments

Write to file a subset of an input stream of sequences
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-exclude]           string     Enter a list of sequence names or accession
                                  numbers to exclude from the sequences read
                                  in. The excluded sequences will be written
                                  to the file specified in the 'junkout'
                                  parameter. The remainder will be written out
                                  to the file specified in the 'outseq'
                                  parameter.
                                  The list of sequence names can be separated
                                  by either spaces or commas.
                                  The sequence names can be wildcarded.
                                  The sequence names are case independent.
                                  An example of a list of sequences to be
                                  excluded is:
                                  myseq, hs*, one two three
                                  a file containing a list of sequence names
                                  can be specified by giving the file name
                                  preceeded by a '@', eg: '@names.dat' (Any
                                  string)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers:
   -junkoutseq         seqoutall  [/dev/null] This file collects the sequences
                                  which you have excluded from the main
                                  output file of sequences.

   Advanced (Unprompted) qualifiers: (none)
   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
   -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
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       string     Output directory

   "-junkoutseq" associated qualifiers
   -osformat           string     Output seq format
   -osextension        string     File name extension
   -osname             string     Base file name
   -osdirectory        string     Output directory
   -osdbname           string     Database name to add
   -ossingle           boolean    Separate file for each entry
   -oufo               string     UFO features
   -offormat           string     Features format
   -ofname             string     Features file name
   -ofdirectory        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

   notseq reads one or more nucleotide 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.fasta

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

   The names (or accession numbers) of the sequences to be excluded can be
   entered as a file of such names by specifying an '@' followed by the
   name of the file containing the sequence names. For example:
   '@names.dat'.

   The names or accession numbers of the sequences to be excluded are not
   standard EMBOSS USAs. Only the ID name or accession number can be
   specified, you cannot specify the sequences as 'database:ID',
   'file:accession', 'format::file', etc.

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.

  Output files for usage example

  File: mydata.seq

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY

  Output files for usage example 2

  File: mydata.seq

>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

  File: hb.seq

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR

Data files

   None.

Notes

   notseq was written for the case where a file containing several
   sequences was being used as a small database, but some of the sequences
   were no longer required. notseq splits the input sequences into those
   that you wish to keep and those you wish to exclude.

   Wildcarded names and accession numbers may be specified in the input
   string by using *.

   The names (or accession numbers) of the sequences to be excluded can be
   entered as a file of such names by specifying an @ followed by the name
   of the file containing the sequence names. For example: @names.dat.

References

   None.

Warnings

   The input string does not support the full USA syntax; only the name or
   accession number should be specified, not the database or file that
   these entries may occur in.

Diagnostic Error Messages

   If no matches are found to any of the specified sequence names, the
   message "This is a warning: No matches found." is displayed.

Exit status

   It exits with a status of 0 unless no matches are found to any of the
   input sequences name, in which case it exits with a status of -1.

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
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   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)

   Gary Williams formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written (9 Jan 2001) - Gary Williams

   Added ability to specify names to exclude as a list file (June 2002) -
   Gary Williams

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
