[ensembl-dev] Question about gene names as queries

[Kieron Taylor]

Based upon the example requests made, the override flag is probably unnecessary. It only exists to allow specifically unusual short requests. FUT2% should not require any such intervention.

Also, watch the single quotes and their effect on variable names within them.

Kieron

On 25 Sep 2012, at 15:16, Brian Osborne wrote:

> 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
>>