[Bioperl-l] DB.t (Bio::DB::Query::GenBank) failures

Baik, Ki ki.baik at roche.com
Wed Apr 18 14:32:35 EDT 2007


I have had similar problems in which a couple of accession numbers out
of a series were not retrieved, yet they do exist in ncbi.

Ki Baik

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Wednesday, April 18, 2007 10:05 AM
To: Sendu Bala
Cc: bioperl-l
Subject: Re: [Bioperl-l] DB.t (Bio::DB::Query::GenBank) failures

I can verify on this end.  Not sure why, but the same accessions are  
used earlier in DB.t tests (Bio::DB::GenBank and get_Stream_by_acc)  
with success.

chris

On Apr 18, 2007, at 11:37 AM, Sendu Bala wrote:

> Hi all,
>
> t/DB.t is currently failing tests 40 and 41:
>
> ok $query = Bio::DB::Query::GenBank->new('-db'  => 'nucleotide',
>                                           '-ids' => [qw(J00522  
> AF303112
> 2981014)],
>                                           -verbose => 1);
>
> cmp_ok $query->count, '>', 0;
>
> You can see that
> http://www.ncbi.nih.gov/entrez/eutils/esearch.fcgi? 
> db=nucleotide&datetype=mdat&usehistory=y&tool=bioperl&term=J00522% 
> 2CAF303112%2C2981014&retmax=100
> gives no results, where presumably it used to give 3. querying on  
> the 3
> ids individually works fine. So... what changed and how do we get  
> around it?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



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