[Bioperl-l] Bio::Perl::get_sequence for Swiss-Prot doesn't work

Chris Fields cjfields at uiuc.edu
Wed Jun 28 16:27:15 EDT 2006


This was a recent bug due to recent changes in EBI's remote database; they
changed the name of the database from 'swall' to 'uniprot'.  Update to
bioperl-live from CVS (or just Bio::DB::SwissProt) and that should fix it.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Amir Karger
> Sent: Wednesday, June 28, 2006 2:50 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Bio::Perl::get_sequence for Swiss-Prot doesn't work
> 
> >perl -MBio::Perl -e '$database="swiss", $id="P09651", $format="fasta";'
> -e '$sequence = get_sequence($database, $id);'
> 
> -------------------- WARNING ---------------------
> MSG: acc (P09651) does not exist
> ---------------------------------------------------
> >perl -MBio::Perl -e '$database="swiss", $id="ROA1_HUMAN",
> $format="fasta";' -e '$sequence = get_sequence($database, $id);'
> 
> -------------------- WARNING ---------------------
> MSG: id (ROA1_HUMAN) does not exist
> ---------------------------------------------------
> 
> But of course, it does exist: http://ca.expasy.org/uniprot/ROA1_HUMAN
> Same error for a couple other proteins.
> Works for a GenBank protein.
> 
> perl 5.8.6
> Perl.pm,v 1.23.2.1 2005/10/09 15:16:18 jason Exp
> 
> This worked a few months ago.
> What's going on?
> 
> -Amir Karger
> 
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