[Bioperl-l] Bio::DB::SwissProt Problem

Chris Fields cjfields at uiuc.edu
Mon Oct 16 14:29:52 EDT 2006


We think there is a problem on the SwissProt (DBFetch) server.  I have
contacted them about the problem and will post something when I hear
something back.

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 Marc Weimer
> Sent: Monday, October 16, 2006 11:44 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Bio::DB::SwissProt Problem
> 
> Dear list members,
> 
> when running
> 
> ######################################################################
> #! /usr/bin/perl -w
> 
> use strict;
> use Bio::DB::SwissProt;
> 
> my $db_obj = new Bio::DB::SwissProt(-verbose => 1);
> 
> my $seq_obj = $db_obj->get_Seq_by_acc("O02938");
> ######################################################################
> 
> using Bioperl 1.5.2 I get the following message:
> 
> ##########################################################################
> ################
> 
> request is POST http://www.ebi.ac.uk/cgi-bin/dbfetch
> Content-Length: 49
> Content-Type: application/x-www-form-urlencoded
> 
> format=swissprot&db=UniProtKB&style=raw&id=O02938
> 
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: acc O02938 does not exist
> STACK: Error::throw
> STACK:
> Bio::Root::Root::throw /usr/local/share/perl/5.8.7/Bio/Root/Root.pm:350
> STACK:
> Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/local/share/perl/5.8.7/Bio/DB/WebDBSeqI.pm:181
> STACK: ./get.test.pl:8
> -----------------------------------------------------------
> 
> ##########################################################################
> ################
> 
> But the accession number does exist. Surprisingly, everything worked
> fine a few days ago. Any ideas of what might have happened?
> 
> Thanks and best regards,
> 
> Marc
> 
> 
> 
> 
> 
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