[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.
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Kieron Taylor PhD.
Ensembl Core software developer

EMBL - European Bioinformatics Institute







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