[ensembl-dev] Gene adaptor returns nothing

[Allan Kamau]

Hi,
I have a list of gene names from EntrezGene for which I would like to
obtain transcripts for.
The code:
@genes=@{ $gene_adaptor->fetch_all_by_external_name('BRCA1') };

returns nothing.

I have composed the test code below mainly from the sample code on the
ensembl api documentation.

What am I overlooking?






use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
-host ='ensembldb.ensembl.org',
-user ='anonymous',
);
if(1==2)
{
	$gene_adaptor=Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "gene"
);
	
	$gene=$gene_adaptor->fetch_by_dbID(1234);
	
	$gene=$gene_adaptor->fetch_by_stable_id('ENSG00000184129');
}

@genes=@{ $gene_adaptor->fetch_all_by_external_name('BRCA1') };

if(1==2)
{
	$slice_adaptor =
	Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "slice" );
	
	$slice =
	$slice_adaptor->fetch_by_region( 'chromosome', '1', 1, 1000000 );
	
	@genes = @{ $gene_adaptor->fetch_all_by_Slice($slice)};
}
while (my $gene = shift @{$genes})
{
	print "Here";
	#$gene.list_stable_ids();
}


Allan.