[Bioperl-l] bioperl-db - Problems when trying to insert GenBank sequence into Pg BioSQL db
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
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);
> 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.
> Chris Goddard
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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