[Bioperl-l] Error retrieving sequence from BioSQL

Hilmar Lapp hlapp at gmx.net
Thu Sep 28 10:04:17 EDT 2006


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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