EMBOSS: notseq

| ## 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