nthseq

Function

Description

In EMBOSS, when an application has to write out many sequences, the normal style is to write them all into one file containing multiple sequences.

This default behaviour can be changed by using the qualifier '-ossingle' which writes many sequences into many files, each containing one sequence.

The program seqretsplit will take a file containing many sequences and will output many files, each containing one sequence. However you have no choice over the naming of the files - they are named after the ID name fo the sequence they contain.

If, however you have the situation where you have a file containing multiple sequences and you wish to extract one of them, then this application may be useful.

nthseq allows you to specify the name of the output file, so you may find that it is useful to include this program in scripts where you need to be able to specify the name of the resulting sequence files you create.

This application extracts the indicated sequence from a multiple set of sequences and writes it out.

Usage

Command line arguments


Input file format

nthseq reads a a normal sequence USA.

Output file format

The output is the specified ordinal sequence from the input USA.

In the example, the second sequence from the input file will be written out to the specified output file.

Data files

None.

Notes

It may be useful to use this application in a small script that extracts all sequences from a multiple sequence file and explicitly names the output files in the way that you require.

For example:

#!/usr/local/bin/perl -w
if ($#ARGV !=1) {
  die "Usage: scriptname in out\n";
}
$count=1;
@list = `infoseq $ARGV[0] -auto -only -name`;
while ($count <= $#list+1) {
  system("nthseq -auto $ARGV[0] -n $count $ARGV[1]-$count.seq");
  $count++;
}

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

The program seqretsplit will take a file containing many sequences and will output many files, each containing one sequence. However you have no choice over the naming of the files - they are named after the ID name fo the sequence they contain.

Author(s)

History

Target users

Comments