EMBOSS: nthseq


Program nthseq

Function

Writes one sequence from a multiple set of sequences

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

Here is a sample session with nthseq.

% nthseq
Input sequence: embl:eclac*
The number of the sequence to output [1]: 2
Output sequence [eclaca.fasta]: 

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -number             integer    The number of the sequence to output
  [-outseq]            seqout     Output sequence USA

   Optional qualifiers: (none)
   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
-number The number of the sequence to output Integer 1 or more 1
[-outseq]
(Parameter 2)
Output sequence USA Writeable sequence <sequence>.format
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

A file containing one or more sequences.

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.

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
infoseqDisplays some simple information about sequences
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
notseqExcludes a set of sequences and writes out the remaining ones
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretallReads and writes (returns) a set of sequences one at a time
seqretsetReads and writes (returns) a set of sequences all at once
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
vectorstripStrips out DNA between a pair of vector sequences

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)

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

History

Written (2000) - Gary Williams

Target users

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

Comments