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 nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
splitterSplit a sequence into (overlapping) smaller sequences
swissparseRetrieves sequences from swissprot using keyword search
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads 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.

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