You can actually do a lot of this more efficiently in BioPerl. So go to CPAN and search for Bundle::BioPerl. There are several types of BioPerl bundels available, but you just want this one for now - the core modules.

You can then code something like this:

use Bio::SeqIO;
$in = Bio::SeqIO->new(-file => '$inputfile',
                      -format => 'fasta');
while (my $seq = $in->next_seq() ) {
    print "fasta tag: ", $seq->id(),
          "sequence: ", $seq->sequence(), "\n";
}

[download]

I think you can figure out how to do the rest of your stuff once you have the fasta tag and the sequence.

In case you don't know about it, check out BioPerl for tutorials, How Do I's and script examples.

Hope this helps...

MadraghRua
yet another biologist hacking perl....

In reply to Re: Problems with Variable Scope in Perl by MadraghRua
in thread Problems with Variable Scope in Perl by InfoSeeker

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