[ensembl-dev] question regarding geneadaptor

Duarte Molha duartemolha at gmail.com
Tue Nov 4 13:33:25 GMT 2014


I am connected to v75


=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================

On 4 November 2014 13:21, mag <mr6 at ebi.ac.uk> wrote:

>  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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