[Bioperl-l] Cannot connect to local ODBA

Brian Osborne brian_osborne at cognia.com
Thu Jun 24 09:21:39 EDT 2004


I believe you've uncovered a sad state of affairs. All protocols in the OBDA
system need to be able to implement a new_from_registry method. The module
that used to do this for the biosql protocol was
Bio::DB::BioSQL::BioDatabaseAdaptor, which no longer exists. This module
uses other modules which also no longer exist, I suspect that simply moving
these older modules back into the Perl directory would not solve the

So at the moment I'd have to say that OBDA does not support the biosql
protocol, someone please correct me if I'm wrong about this. If this is the
case then I'll change the documentation to indicate that the biosql protocol
is not supported. I could take a shot at getting it running again but
someone first must confirm if my suspicion is correct, or point me in the
right direction.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Andy Hammer
Sent: Wednesday, June 23, 2004 6:50 PM
To: bioperl
Subject: [Bioperl-l] Cannot connect to local ODBA

I have altered the sample code from the ODBA HOWTO as

#use strict;
use Bio::Perl;
use Bio::DB::Registry;

$registry = Bio::DB::Registry->new;
$db = $registry->get_database('ncbi');
$seq = $db->get_Seq_by_acc('NM_000367');
print $seq->seq,"\n";

my seqdatabase.ini contains:

But I get the error:
Can't call method "seq" on an undefined value at
./testdb.pl line 10, <FH> line 20.

I don't think it is connecting to my local db.  The
sample code that points to embl works fine.  My local
biosql database is called ncbi and it loaded fine
using load_seqdatabase.pl provided with bioperl-db.
Any ideas?

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