[Bioperl-l] retrieving top_SeqFeatures for RefSeq proteins fails

Chris Fields cjfields at uiuc.edu
Tue Apr 11 18:06:57 EDT 2006


I'll look into it tomorrow, but you might try updating to 1.5.1 or CVS to
see if it helps.

Chris

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Eleni Rapsomaniki
> Sent: Tuesday, April 11, 2006 2:31 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] retrieving top_SeqFeatures for RefSeq proteins
> fails
> 
> Hi again,
> 
> Thank you for your reply regarding the retrieval of sequence features for
> Refseq proteins. I have updated to bioperl 1.5 but the re-direct still
> does not
> work and the following code:
> 
> my $factory = Bio::DB::GenBank->new(-no_redirect => 1);
> my $seq = $factory->get_Seq_by_acc(' NM_001008292');
> 
> returns:
> MSG: [gb| NM_001008292] is not a normal sequence entry but a RefSeq entry.
> Redirecting the request.
> 
> -------------------- WARNING ---------------------
> MSG: acc (gb| NM_001008292) does not exist
> ---------------------------------------------------
> 
> I get the same error when I replace Bio::DB::GenBank with Bio::DB::RefSeq,
> and
> with many other refseq accessions.
> 
> Could I be doing something wrong or maybe I should be using a different
> method
> for parsing refseq records? I suppose the alternative is to create objects
> from
> files after fetching them..
> 
> Many thanks
> Eleni Rapsomaniki
> 
> 
> 
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