
                                  notseq 



Function

   Excludes a set of sequences and writes out the remaining ones

Description

   When you have a set of sequences (a file of multiple sequences?) and
   you wish to remove one or more of them from the set, then use notseq.

   This program was written for the case where a file containing several
   sequences is being used as a small database, but some of the sequences
   are no longer required and must be deleted from the file.

   notseq splits the input sequences into those that you wish to keep and
   those you wish to exclude.

   notseq takes a set of sequences as input together with a list of
   sequence names or accession numbers. It also takes the name of a new
   file to write the files that you want to keep into, and optionally the
   name of a file that will contain the files that you want excluded from
   the set.

   notseq then reads in the input sequences. It outputs the ones that
   match one of the sequence names or acession numbers to the file of
   excluded sequences, and those that don't match are output to the file
   of sequences to be kept.

   Note that the names of the sequences to be excluded are not standard
   EMBOSS USAs. Only the name or accession number shoudl be specified,
   not the database or file that these entries may occur in. These
   excluded sequence names will be matched against the names of the input
   sequences to see if there is a match. Wildcarded names may be
   specified by using '*'s. Any specified names of sequences to be
   excluded that are not found are simply ignored.

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 
Excludes a set of sequences and writes out the remaining ones
Input sequence(s): globins.fasta
Sequence names to exclude: myg_phyca,lgb2_luplu
Output sequence [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 
Excludes a set of sequences and writes out the remaining ones
Input sequence(s): globins.fasta
Sequence names to exclude: hb*
Output sequence [hbb_human.fasta]: mydata.seq

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database 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'
  [-outseq]            seqoutall  Output sequence(s) USA

   Additional (Optional) qualifiers:
   -junkoutseq         seqoutall  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
   -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
   -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 standard output
   -filter              boolean    Read standard input, write 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. 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-exclude]
   (Parameter 2) 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 is accepted An empty string is
   accepted
   [-outseq]
   (Parameter 3) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Additional (Optional) qualifiers Allowed values Default
   -junkoutseq This file collects the sequences which you have excluded
   from the main output file of sequences. Writeable sequence(s)
   /dev/null
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   notseq reads normal sequence USAs.

  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

   notseq writes normal a sequence file.

  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

   Note that 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.

References

   None.

Warnings

   None.

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
   biosed       Replace or delete sequence sections
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   skipseq      Reads and writes (returns) sequences, skipping the first few
   splitter     Split a sequence into (overlapping) smaller sequences
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file

Author(s)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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
