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

Marc Weimer m.weimer at dkfz-heidelberg.de
Mon Oct 16 12:43:38 EDT 2006


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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