Note how simple the BioPerl solution is. 

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file   => "933212.txt" ,
                           -format => 'fasta');

my $out_seq = Bio::SeqIO->new( -file   => '>sequence.dat',
                               -format => 'fasta');

my $out_secstr = Bio::SeqIO->new( -file   => '>secstr.dat',
                                  -format => 'fasta');

while ( my $seq = $in->next_seq() ) {
    if ($seq->id =~ /sequence$/) {
        $out_seq->write_seq($seq);
    }
    elsif ($seq->id =~ /secstr$/) {
        $out_secstr->write_seq($seq);    
    }
}

[download]

Chris

In reply to Re: How to match the sequences with headers by Cristoforo
in thread How to match the sequences with headers by anonym

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.