[ensembl-dev] Gene adaptor returns nothing

[Allan Kamau]

On 5/22/12, Andy Yates <ayates at ebi.ac.uk> wrote:
> 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.
>>
>> _______________________________________________
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>
>
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>


Thank you Andy, the code you provided has solved my issue.

Allan.