[Bioperl-l] bioperl-db - Problems when trying to insert GenBank sequence into Pg BioSQL db

Hilmar Lapp hlapp at gmx.net
Wed Apr 8 12:21:11 EDT 2009

This all sounds like you aren't issuing commit. Are you sure your code  
contains $popj->commit() and what you are looking at is *after* that  
is executed?

Bioperl-db is transactional, so you decide when to commit (or rollback).


On Apr 8, 2009, at 11:25 AM, Chris Goddard wrote:

> I am running into problems when trying to insert a sequence object  
> retrieved from GenBank into a BioSQL schema running in a Postgres  
> database.  Whenever I use the 'create()' method on the sequence that  
> has been made into a persistent object, the sequence isn't saved  
> into the database properly.  No error messages are given, and the  
> corresponding Postgres primary key sequences are incremented as if  
> the data had been saved properly: the appropriate tables themselves  
> remain empty though.
> I am completely new to using the biosql-db modules, and so am  
> probably missing something pretty simple.  Below you will see the  
> basic code that causes the problem.
> my $genbank_id = 'AYXXXXXX'
> my $genDB = new Bio::DB::GenBank;
> $sequence = $genDB->get_Seq_by_id($genbank_id);
> my $db = Bio::DB::BioDB->new(-database => 'biosql',
>                            -user => 'username',
>                            -dbname => 'dbname',
>                            -host => 'localhost',
>                            -driver => 'Pg');
> my $pobj = $db->create_persistent($sequence);
> $pobj->create();
> I am running the latest svn trunk versions of bioperl and bioperl-db  
> (as of yesterday) and Postgres 8.3.7.  I also downloaded the NCBI  
> taxonomy info using the script included in the BioSQL package, and  
> that data seemed to install without error.  Any help or advice would  
> be greatly appreciated.
> Thanks,
> Chris Goddard
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> Bioperl-l at lists.open-bio.org
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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