[ensembl-dev] Havana Gene in Compara

Nick Fankhauser lists at nyk.ch
Tue May 10 16:13:20 BST 2011

I'm trying to get a member adaptor for Havana Genes (ncRNAs), for 
example OTTHUMG00000002858.
The following script works for Ensembl Genes, but how do I have to 
formulate it for Havana Genes?

use lib "/opt/ensembl/modules";
use lib "/opt/ensembl-compara/modules";
use strict;
use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(-host => 
'ensembldb.ensembl.org', -user => 'anonymous');
my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 
'compara', 'Member');
throw("Cannot connect to Compara") if (!$member_adaptor);

# works:
my $member = 
die("Gene not found!") if (!$member);
print $member->description,"\n";

# does not work:
my $member = 
die("Gene not found") if (!$member);
print $member->description,"\n";

The program dies on the second "fetch_by_source_stable_id" for 
OTTHUMG00000002858. How can I fetch an adaptor for it?

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