[ensembl-dev] question regarding geneadaptor

[mag]

Hi Duarte,

Can you check which database you are connecting to?

I tried the following:
my $registry = "Bio::EnsEMBL::Registry";
$registry->load_registry_from_db(
-db_version => 77,
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-port => '3337',
);

my $query_gene = "CYP2D7P";
my $gene_adaptor = $registry->get_adaptor('human', 'core', 'gene');
print "Using database " . $gene_adaptor->dbc->dbname() . "\n";
my @fetched_genes = 
@{$gene_adaptor->fetch_all_by_display_label($query_gene)};
foreach my $gene (@fetched_genes) {
   print "Found " . $gene->stable_id . " with name " . 
$gene->display_xref->display_id . "\n";
}

And got the following results:
Using database homo_sapiens_core_77_37
Found ENSG00000205702 with name CYP2D7P
Found ENSG00000263181 with name CYP2D7P

This also works on the live GRCh38 database.


Regards,
Magali

On 04/11/2014 12:03, Duarte Molha wrote:
> Dear developer
>
> I have simple script to fetch gene information and I am having 
> problems with a particular gene that I know is correct and on the 
> database:
>
> http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000205702;r=22:42536214-42540576
>
> here is the code I use to fecth it:
>
> $query_gene = "CYP2D7P";
>
> my @fetched_genes = 
> @{$gene_adaptor->fetch_all_by_display_label($query_gene)};
>
> however ...
>
> this method returns an empty list.
>
> Why is this?
>
>
> I have also tried:
>
> my @fetched_genes =  @{ 
> $gene_adaptor->fetch_all_by_external_name($query_gene) };
>
> and this also fails.
>
> Can someone tell me what I am doing wrong?
>
>
> Best regards
>
> Duarte
>
>
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