Jason Gallant | 4 Dec 21:23 2012

Problem with BIO::DB::FASTA and Colon in Fasta Header


I'm trying to retreive fasta sequences that contain a colon in their 
header.  However, I cannot get my BioPerl script to do this!!

It works as expected when the header does not contain the colon, however 
doesn't return anything when it does.  Weirdly, when I ask it to return the 
parsed IDs (see below), it returns the appropriate IDs, which include the 
colon!  Very confusing, would appreciate any help!!

Many Thanks,
Jason Gallant

use strict;
use Bio::SearchIO; 
use Bio::DB::Fasta;

my ($file,$id,$start,$end) = 

my $db = Bio::DB::Fasta->new($file, -reindex=>1);
my $seq = $db->seq($id,$start,$end);

print $db->ids;

print $seq,"\n";