[Bioperl-l] parsing kegg 'ko' file

shalabh sharma shalabh.sharma7 at gmail.com
Fri Jan 20 16:22:30 EST 2012


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> 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] 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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