[Bioperl-l] parsing kegg 'ko' file

[KARALIUS, JOSEPH (AG/2401)]

Shalabh,

Your print statement should look something like this (not tested).

my  $ann = $seq->annotation();
foreach my $desc ($ann->get_Annotations('description')) {
     print $desc->title, "\n";
}


See 'perldoc Bio::Seq'.

Joey


From: shalabh sharma [mailto:shalabh.sharma7 at gmail.com]
Sent: Friday, January 20, 2012 1:23 PM
To: KARALIUS, JOSEPH [AG/2401]
Cc: bioperl-l
Subject: Re: [Bioperl-l] parsing kegg 'ko' file

Hi Joseph,
              Thanks a lot, i am feeling so stupid right now..
But when i again ran that code i got following output:

Bio::PrimarySeq=HASH(0x9be888) E3.2.1.1, amyA, malS Bio::Annotation::Comment=HASH(0x9c2484)
Bio::PrimarySeq=HASH(0x9be930) E3.2.1.2 Bio::Annotation::Comment=HASH(0x9be8c4)

How come i am getting object ? Only name filed is fine.
I would really appreciate your help.

Thanks
Shalabh


On Fri, Jan 20, 2012 at 4:07 PM, KARALIUS, JOSEPH (AG/2401) <joseph.karalius at monsanto.com<mailto:joseph.karalius at monsanto.com>> wrote:
'pimary_id' should be 'primary_id'.

Cheers,
Joey

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org> [mailto: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

Thanks
Shalabh

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