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

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Mon Aug 9 04:52:42 EDT 2004


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


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   =>
					           -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()) {

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
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?


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