[BioSQL-l] GBrowse on BioSQL dead in water again

[Lincoln Stein]

Hi Elia,

Alas, the latest CVS update of bioperl-db removed the
Bio::DB::BioSQL::BioDatabaseAdaptor module, and so broke the
Bio::DB::Das::BioSQL module that was dependent upon it.  There is no
obvious documentation of what the preferred interface now is.  Could
you show me how to rewrite the following script for me to use the
approved API?

I had been running GBrowse very happily on top of it until now, but
I'm afraid that it is now dead in the water.

Thanks,

Lincoln

-----------

#!/usr/bin/perl

use Bio::DB::BioSQL::BioDatabaseAdaptor;
use Bio::DB::BioSeqDatabase;

my $dbc = Bio::DB::BioSQL::BioDatabaseAdaptor->new_from_registry(
						    driver   => 'mysql',
						    dbname => 'biosql',
						    biodbname => 'test',
						    host   => 'localhost',
						    user   => 'lstein',
						    pass   => undef,
						    port   => undef,
			     );
my @seq = $dbc->get_all_primary_ids;
print "got @seq\n";

my $thing = $dbc->get_Seq_by_acc($seq[0]);
print "got $thing\n";

my @a = $thing->top_SeqFeatures;

my $ad = $dbc->_adaptor;
print $ad->list_bioentry_ids('test'),"\n";

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
========================================================================