[ensembl-dev] Gene adaptor returns nothing
Andy Yates
ayates at ebi.ac.uk
Tue May 22 12:23:33 BST 2012
Hi Allan,
I think you were having some issues with the hash assignment parameter in the call to the registry. Please see a working version of your script below:
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
# The hash assignment here should be => & not = as you had it
Bio::EnsEMBL::Registry->load_registry_from_db(
-host =>'ensembldb.ensembl.org',
-user =>'anonymous',
);
my $gene_adaptor=Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "gene");
#If you want genes based on a single DB then specify it as the second parameter to this method. We support wildcards here as well
my @genes=@{ $gene_adaptor->fetch_all_by_external_name('BRCA1', 'EntrezGene') };
while (my $gene = shift @genes) {
print $gene->stable_id(), "\n";
}
All the best,
Andy
Andrew Yates Ensembl Core Software Project Leader
EMBL-EBI Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensembl.org/
On 22 May 2012, at 12:05, Allan Kamau wrote:
> 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.
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
More information about the Dev
mailing list