Home
Reading
Searching
Subscribe
Sponsors
Statistics
Posting
Contact
Spam
Lists
Links
About
Hosting
Filtering
Features Download
Marketing
Archives
FAQ
Blog
 
Gmane
From: Jason Gallant <jason.r.gallant <at> gmail.com>
Subject: Problem with BIO::DB::FASTA and Colon in Fasta Header
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Tuesday 4th December 2012 20:23:02 UTC (over 4 years ago)
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";
 
CD: 2ms