[Bioperl-l] Problem retrieving peptides using GenPept

[Palle Villesen]

Hi,

I have the following code (below), but I get the following error and I'm 
stuck. I have tried various queries and I always get <300 seqs back 
before the exception occurs. I'm not sure if it a speed problem, i.e. 
retrieving the datastream quickjly enough, but I have tried the 
-retrievaltype=>'tempfile' as well - which didn't help.

I couldn't find anything in the docs, hence this mail. Sorry to disturb.

Greetings,
P.
--

   Palle Villesen, Ph.D. 
   BiRC, Build. 090, University of Aarhus
   DK - 8000 Aarhus C, Denmark

   Http://www.daimi.au.dk/~biopv - +45 61708600
---------------------------------------------------------------------



OUTPUT:

Getting accession number for the following query:
BSE

Hits: 118
1 Seq length 176
2 Seq length 253
3 Seq length 176
4 Seq length 178
5 Seq length 96
6 Seq length 179
7 Seq length 179
8 Seq length 253
9 Seq length 360

-------------------- WARNING ---------------------
MSG: exception while parsing location line [bond(179,214)] in reading 
EMBL/GenBank/SwissProt, ignoring feature Bond (seqid=Q60506):
------------- EXCEPTION  -------------
MSG: operator "bond" unrecognized by parser
STACK Bio::Factory::FTLocationFactory::from_string 
/home/serine/palle/bioperl-live/Bio/Factory/FTLocationFactory.pm:160
STACK (eval) /home/serine/palle/bioperl-live/Bio/SeqIO/FTHelper.pm:124
STACK Bio::SeqIO::FTHelper::_generic_seqfeature 
/home/serine/palle/bioperl-live/Bio/SeqIO/FTHelper.pm:123
STACK Bio::SeqIO::genbank::next_seq 
/home/serine/palle/bioperl-live/Bio/SeqIO/genbank.pm:396
STACK main::get_query get_RVproteins_from_GB.pl:30
STACK (eval) get_RVproteins_from_GB.pl:8
STACK toplevel get_RVproteins_from_GB.pl:7

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

---------------------------------------------------
Caught exception
Done


Program:

#!/usr/local/bin/perl
my $query_string = "BSE";

print "Getting the following query:$query_string\n";

eval {
  get_query($query_string);
};

if ($@) {
  print "Caught exception\n";
}
print "Done\n\n";
exit();

sub get_query {
  use Bio::DB::GenPept;
  use Bio::DB::Query::GenBank;
  my ($query_string) = @_;
  my $query = Bio::DB::Query::GenBank->new(-db=>'protein',
					   -query=>$query_string
					  );
  my $gb = Bio::DB::GenPept->new ();
  print "Hits: ".$query->count."\n";
  my @ids = $query->ids;
  my $current =1;
  my $seqio = $gb->get_Stream_by_query($query);
  my $current =1;
  while (my $seq = $seqio->next_seq()) {
    print $current++." Seq length ".$seq->length()."\n";
  }
return 1;
}