[ensembl-dev] Question about gene names as queries

[Brian Osborne]

Kieron,

Very nice. So something like:

      my $gene = $gene_adaptor->fetch_all_by_external_name('$id%',,1);

Should work and the wild-card will be used?

Thanks again,

Brian O.


On Sep 25, 2012, at 9:46 AM, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> 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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