[Bioperl-l] parsing kegg 'ko' file

KARALIUS, JOSEPH (AG/2401) joseph.karalius at monsanto.com
Fri Jan 20 16:07:03 EST 2012

'pimary_id' should be 'primary_id'.


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of shalabh sharma
Sent: Friday, January 20, 2012 12:43 PM
To: bioperl-l
Subject: [Bioperl-l] parsing kegg 'ko' file

Hi All,
        I am trying to parse kegg 'ko' file. I just need three information
out of it.
name, entry and description, so i just wrote this small code:

#!/usr/bin/perl -w
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-file => "ko", -format => 'KEGG');
while(my $seq = $in->next_seq){
      print $seq->pimary_id, "\t" ;
      print $seq->display_id, "\t";
      print $seq->annotation->get_Annotations('description') ,"\n";

But when i tried to run this i got this error:
Can't locate object method "pimary_id" via package "Bio::Seq::RichSeq" at
parseKO_bioperl.pl line 5, <GEN0> line 1.
I am using bioperl -v 1.006001


Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636
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