[ensembl-dev] Question about gene names as queries
Kieron Taylor
ktaylor at ebi.ac.uk
Tue Sep 25 14:46:07 BST 2012
Hi Brian,
If you treat your display id as an external name, you'll find things a lot easier. Ensembl display labels are not necessarily the same as globally recognised labels, or rather there are things with display labels that are not currently named by convention.
Take a look at fetch_all_by_external_name() on the Gene Adaptor. There is a small performance penalty involved.
Kieron
On 25 Sep 2012, at 14:29, Brian Osborne wrote:
> To whom it may concern,
>
> I'm writing simple code using the most recent Perl API, this code downloads sequences using read-able id's like "FUT2". I noticed that when I use this id as a query at ensembl.org I retrieve ~20 genes, and the names of these genes are all "FUT2" except for the chimp gene, which is named "FUT2_PANTR". My code has lines like this:
>
> my $gene_adaptor = $registry->get_adaptor( $species, 'Core', 'Gene' );
> my $gene = $gene_adaptor->fetch_by_display_label($id);
>
> I would like to be able to loop over all the species (Human, Pig, Chimpanzee, etc.) and get all the FUT2 sequences but I can't get the chimp sequence since wild-cards don't work here (e.g. "$id%").
>
> Your thoughts?
>
> Thank you,
>
> Brian O.
> _______________________________________________
> 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/
Kieron Taylor PhD.
Ensembl Core software developer
EMBL - European Bioinformatics Institute
More information about the Dev
mailing list