[Bioperl-l] Error retrieving sequence from BioSQL

Chris Fields cjfields at uiuc.edu
Thu Sep 28 10:19:36 EDT 2006


I had problems with bioperl-db on native WinXP (not cygwin), but I  
did manage to get it running in cygwin with some effort.  The issue  
on native WinXP was related to Bio::Root::Root::throw(), though.

There is a bug and workaround filed on Bugzilla, but I haven't worked  
on it in a while (and the workaround has some problems as well).  I  
may try running it again to see what happens.

http://bugzilla.open-bio.org/show_bug.cgi?id=1938

Chris

On Sep 28, 2006, at 9:04 AM, Hilmar Lapp wrote:

> Very odd. This is under Windows, presumably using Cygwin?
>
> The method Bio::Root::Root::throw() clearly exists, and
> PersistentObject inherits from it. The exception it was trying to
> throw has nothing to do with failure or success to find the database
> row (actually it did succeed since otherwise it wouldn't construct
> the object) but with dynamically loading a class, presumably
> Bio::DB::Persistent::Seq.
>
> Are you using the 1.5.x release of bioperl?
>
> Does anyone on the list have any experience with these sorts of
> things on Windows?
>
> (Seth, I've moved this thread to the bioperl list, since this is what
> the problem is about.)
>
> 	-hilmar
>
> On Sep 27, 2006, at 1:39 PM, Seth Johnson wrote:
>
>> Hello guys,
>>
>> I successfully populated the biosql database, thanks to you.  Now,  
>> I'm
>> trying to retrieve a sequence from it following the example from
>> BOSC2003
>> slides and ran into uninformative error (at least to me it doesn't
>> mean
>> anyting).  I suspect that I'm missing something and hope you can
>> point me in
>> the right direction.  Here's my source code:
>> --------------------------------------------------------------------- 
>> -
>> ---
>> #!/usr/bin/perl -w
>> use strict;
>> use warnings;
>>
>> use Bio::Seq;
>> use Bio::Seq::SeqFactory;
>> use Bio::DB::SimpleDBContext;
>> use Bio::DB::BioDB;
>>
>> my $dbc = Bio::DB::SimpleDBContext->new(
>>     -driver => 'mysql',
>>     -dbname => 'BioSQL_1',
>>     -host => '192.168.1.3',
>>     -user => 'xxxxx',
>>     -pass => 'xxxxxx'
>> );
>>
>> my $db = Bio::DB::BioDB->new(-database  => 'biosql',
>>                             -dbcontext => $dbc);
>>
>> my $seq = Bio::Seq->new(-accession_number => 'NM_014580', -
>> namespace =>
>> 'refseq_H_sapiens');
>> my $seqfact = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq');
>> my $adp = $db->get_object_adaptor($seq);
>> my $dbseq = $adp->find_by_unique_key($seq, -obj_factory => $seqfact);
>>
>> my $out = Bio::SeqIO->newFh('-format' => 'EMBL');
>> print $out $dbseq;
>>
>> exit;
>> -----------------------------------------------------------------
>>
>> Just when the "find_by_unique_key" function is executed I get the
>> following
>> error:
>>
>> ================================
>> Undefined subroutine &Bio::Root::Root::throw called at
>> c:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm line 199.
>> ================================
>>
>> The sequence does exist in the database. I checked that.  Any  
>> ideas???
>>
>> -- 
>> Best Regards,
>>
>>
>> Seth Johnson
>> Senior Bioinformatics Associate
>> _______________________________________________
>> BioSQL-l mailing list
>> BioSQL-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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