[Bioperl-l] Entrez interface for NT contigs

[Neill White]

Hello,

My problem is that I'm unable to retrieve the NT con sequences
through the entrez interface.  The error I get is:

-------------------- WARNING ---------------------
MSG: CONTIG found. GenBank get_Stream_by_acc about to run.
---------------------------------------------------
Warning: unable to close filehandle FETCH properly.

------------- EXCEPTION  -------------
MSG: in subseq, start [111855] has to be greater than end [106558]
STACK Bio::PrimarySeq::subseq /usr/lib/perl5/site_perl/5.6.0/Bio/PrimarySeq.pm:358
STACK Bio::Seq::subseq /usr/lib/perl5/site_perl/5.6.0/Bio/Seq.pm:635
STACK Bio::DB::NCBIHelper::postprocess_data
/usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm:329
STACK Bio::DB::WebDBSeqI::_stream_request /usr/lib/perl5/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:687
STACK Bio::DB::WebDBSeqI::get_seq_stream /usr/lib/perl5/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:434
STACK Bio::DB::NCBIHelper::get_Stream_by_query
/usr/lib/perl5/site_perl/5.6.0/Bio/DB/NCBIHelper.pm:249
STACK toplevel ./dump_gene_annotation.pl:32

and the offending code is:

     24 my $gb = new Bio::DB::GenBank;
     25
     26 # get a stream via a query string
     27 my $query_string = $gene_name . '[gene] AND Human[Organism] AND contig';
     28 my $query = Bio::DB::Query::GenBank->new
     29     (-query   => $query_string,
     30      -db      => 'nucleotide');
     31
     32 my $seqio = $gb->get_Stream_by_query($query);

The documentation recommends that for contigs, to put a 

    $gb->request_format('fasta')

before making the query, but it's really not the sequence I want - 
it's the annotation.

Any help would be much appreciated.

-neill

__________________________________
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search
http://shopping.yahoo.com