[Bioperl-l] Extracting gi no from refseq record

[Hilmar Lapp]

Siddharta, which version of bioperl are you using? The GI number being 
made available via $seq->primary_id() is only there since 1.2.

The method to call is primary_id(), not display_id().

	-hilmar

On Thursday, April 3, 2003, at 07:07  AM, Siddhartha Basu wrote:

> Hi,
> I am trying to extract the gi no from the refseq flat files that is in 
> genbank format. This is what i have done so far...
>
> *** Indexed the files with Bio::Index::GenBank module
> *** Then try to fetch a particular entry by get_Seq_by_acc/id call.
> *** It returns a Bio::Seq::RichSeq object.
> *** Now i have tried to get the gi no by
> *** $Seq->primary_id(), $Seq->display_id() calls but both of them 
> return
> the locus name. Since $Seq is a RichSeq object i have also tried with 
> $Seq->pid() call but nothing happens.
>
>
> So, how is it possible to extract that number for a particular NP or 
> NM refseq number specially from flat files.
>
>
> siddhartha
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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