[ensembl-dev] Question about gene names as queries

Brian Osborne bosborne11 at verizon.net
Tue Sep 25 14:29:51 BST 2012


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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