
                               EMBOSS: notseq
     _________________________________________________________________
   
                                Program 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.
   
Usage

   Here is a sample session with notseq. In this case the excluded
   sequences ('clone186' and 'clone876') are simply thrown away and not
   saved to any file.
   
% notseq
Input sequence(s): mydata.seq
Output sequence [clone001.fasta]: mydata2.seq
Sequence names to exclude: clone186, clone876

   Here is an example where the sequences to be excluded are saved to
   another file:
   
% notseq -junkout excluded.seq
Input sequence(s): mydata.seq
Output sequence [clone001.fasta]: mydata2.seq
Sequence names to exclude: clone99*

Command line arguments

   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
  [-outseq]            seqoutall  Output sequence(s) USA

   Optional qualifiers:
   -junkout            seqoutall  This file collects the sequences which you
                                  have excluded from the main output file of
                                  sequences.

   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   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 Any string is accepted An empty
   string is accepted
   [-outseq]
   (Parameter 3) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Optional qualifiers Allowed values Default
   -junkout This file collects the sequences which you have excluded from
   the main output file of sequences. Writeable sequence(s) /dev/null
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Normal sequence USA.
   
Output file format

   Normal sequence USA.
   
Data files

   None.
   
Notes

   None.
   
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
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   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)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Written (9 Jan 2001) - Gary Williams
   
Target users

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