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

Marc Weimer m.weimer at dkfz-heidelberg.de
Thu Oct 5 08:15:53 EDT 2006


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('P43780');


-------------------------------------------------------------

using Bioperl 1.4-1 I get the error message

---------------------------------------------------------------------------------

  request is POST http://www.ebi.ac.uk/cgi-bin/dbfetch
  Content-Length: 45
  Content-Type: application/x-www-form-urlencoded

  format=swissprot&db=swall&style=raw&id=P43780


  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG: swissprot stream with no ID. Not swissprot in my book
  STACK: Error::throw
  STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
  STACK
Bio::SeqIO::swiss::next_seq /usr/share/perl5/Bio/SeqIO/swiss.pm:179
  STACK:
Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:187
  STACK: ./putativeGele.pl:8
  -----------------------------------------------------------

--------------------------------------------------------------------------------

Any suggestions?

Thanks,

Marc






More information about the Bioperl-l mailing list