[Bioperl-l] bioperl-db - Problems when trying to insert GenBank sequence into Pg BioSQL db
Chris Goddard
cgoddard at flmnh.ufl.edu
Wed Apr 8 15:25:37 UTC 2009
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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