[Bioperl-l] bioperl-db - Problems when trying to insert GenBank sequence into Pg BioSQL db
cgoddard at flmnh.ufl.edu
Wed Apr 8 12:30:24 EDT 2009
That was it. I guess I just incorrectly assumed that create() did an
auto-commit. That was simple to fix. Thank you!
Hilmar Lapp wrote:
> 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);
>> 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
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