Apologies for cross posting from StackExchange- perhaps this is the more appropriate venue. I'm trying to extract the sequence I need from a database using the following bioperl code:
use strict; use Bio::SearchIO; use Bio::DB::Fasta; my ($file, $id, $start, $end) = ("secondround_merged_expanded.fasta","C7136661:0-107",1,10); my $db = Bio::DB::Fasta->new($file); my $seq = $db->seq($id, $start, $end); print $seq,"\n";
Where the header of the sequence I'm trying to extract is:
C7136661:0-107, as in the file:
The code extracts the appropriate sequence when the header and $id in above is changed to
I'm thinking that BioPerl doesn't like the heading with the colon. Any way to fix this so I don't have to recode the FASTA files?