[Bioperl-l] Problems retrieving sequences with Bio::DB::Query::GenBank

[michael watson (IAH-C)]

Hi

I am having a few problems with Bio::DB::Query::GenBank (Bioperl 1.4,
Suse Linux).  Here is my script:

#!/usr/bin/perl

use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use Bio::DB::GenBank;

my $query_string = 'Avian infectious bronchitis virus [Organism]';
my $query = Bio::DB::Query::GenBank->new(-db      => 'nucleotide',
					           -query   =>
$query_string,
					           -verbose => 0);

my $count = $query->count;
print "Query has $count sequences\n";

my $db = new Bio::DB::GenBank;
my $stream = $db->get_Stream_by_query($query);

my $out  = Bio::SeqIO->new(-format   => 'Fasta' ,
			   -file     => '>out.fasta');

while (my($seq) = $stream->next_seq()) {
	$out->write_seq($seq);
}

So this is all "by the book" code, mostly taken directly from the docs.

What happens is that out.fasta fills up with 500 sequences (there should
be 810) and then I get an error:

------------- EXCEPTION  -------------
MSG: Did not provide a valid Bio::PrimarySeqI object
STACK Bio::SeqIO::fasta::write_seq
/usr/local/bioperl-1.4/Bio/SeqIO/fasta.pm:178
STACK toplevel scripts/get_seqs.pl:26

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

Speaking from personal experience, I have never been able to get the
"get_stream_by..." methods to work.

Does anyone have a clue what might be going wrong?

Thanks
Mick