
                               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 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
   notseq       Excludes a set of sequences and writes out the remaining ones
   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
   
   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
