4 Dec 2012 21:23
Problem with BIO::DB::FASTA and Colon in Fasta Header
Jason Gallant <jason.r.gallant <at> gmail.com>
2012-12-04 20:23:02 GMT
2012-12-04 20:23:02 GMT
Hello,
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) =
("secondround_merged_expanded.fasta","C7047455:0-100",1,10);
my $db = Bio::DB::Fasta->new($file, -reindex=>1);
my $seq = $db->seq($id,$start,$end);
print $db->ids;
print $seq,"\n";
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