[ensembl-dev] getting EntrezGene IDs from Ensembl $gene
ian Longden
ianl at ebi.ac.uk
Tue Sep 14 16:10:32 BST 2010
use get_all_DBLinks method from the gene :-)
You can also pass it the database name too this will reduce the number
of entries returned
i.e.
foreach my $dbe ($gene->get_all_DBLinks("EntrezGene")){
-Ian
On Tue, Sep 14, 2010 at 3:12 PM, Sergei Manakov <manakov at ebi.ac.uk> wrote:
> Hello,
>
> I found a way of getting EntrezGene IDs from $translation (the code is
> below), but is there a way of getting EntrezGene IDs directly from
> $gene ?
>
> thanks,
> Sergei
>
>
> foreach my $transcript (@{$gene->get_all_Transcripts}) {
> my $translation = $transcript->translation;
> if (defined $translation) {
> my $tln_dbentries = $translation->get_all_DBEntries;
> foreach my $dbe (@$tln_dbentries) {
> if ($dbe->dbname eq 'EntrezGene') {
> print $dbe->primary_id, "\t";
> }
> }
> }
> }
>
>
>
>
>
> --
> EMBL-EBI and Wellcome Trust Sanger Institute
>
> tel: 00441223492675
>
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