[Bioperl-l] A problem on BioPerl module Bio::DB::Fasta

Tao Zhu bill_zt at sina.com
Tue Oct 26 21:08:11 EDT 2010

Hello, everyone!

I hope it isn't true, but I really find a problem on BioPerl module
Bio::DB::Fasta. In http://www.bioperl.org/wiki/HOWTO:Beginners Brian
Osborne wrote that we could catch sub-sequences like this,

use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seqobj = $db->get_Seq_by_id($id,$start,$end);
print $seqobj->seq,"\n";

In fact it didn't work. I only got the whole sequence after running the
script. Therefore I referred to the Pdoc documentation and realized it
should be written as follows,

use Bio::DB::Fasta;
($file,$id,$start,$end) = ("genome.fa","CHROMOSOME_I",6,10);
$db = Bio::DB::Fasta->new($file);
$seq = $db->seq($id,$start,$end);
print $seq,"\n";

Then it would return the sub-sequence from 6 to 10.

Probably Dr Osborne had made a mistake when writing the use-guide

Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
email: tzhu at mail.bnu.edu.cn

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