[Bioperl-l] How to retrieve a persistent object by bioperl-db?

Hilmar Lapp hlapp at gmx.net
Sun Jan 6 22:02:32 EST 2008


Hi Zhihua, you didn't ever respond to Marc's link to the Persistent  
Bioperl slides - did that help?

	-hilmar

On Dec 6, 2007, at 11:25 PM, zhihuali wrote:

>
> Hi netters,
>
> I've installed BioSQL and bioperl-db, and successfully created and  
> stored a persistent object:
>
> use strict;use warnings;use Bio::Seq;use Bio::DB::BioDB;
> my $dbadp=Bio::DB::BioDB->new(- 
> database=>'biosql',                             - 
> user=>'annoymous',                             -dbname=>'bioseqdb');
>
> my $seqobj=Bio::Seq->new(- 
> accession_number=>"test",                      - 
> id=>"test1",                      - 
> seq=>"AGCTAGCT",                      -version=>1);my $dbobj=$dbadp- 
> >create_persistent($seqobj);$dbobj->create;$dbobj->commit;
>
> It's successful because I found corresponding rows in the bioseqdb  
> tables.
>
> Now I want to retrieve the object back from the database. There's  
> not much documents available and I've tried find_by_unique_key/ 
> primary_key but all failed. Maybe I didn't use them correctly.  
> Could anyone give me an example as how to retrieve the stored  
> Bio::Seq object?
>
> Thanks a lot!
>
> Zhihua Li
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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