[ensembl-dev] Question about gene names as queries

[Brian Osborne]

Very good, that works!

On Sep 25, 2012, at 10:30 AM, Andreas Kusalananda Kähäri <ak4 at sanger.ac.uk> wrote:

> Also, the method returns a list reference (to a list of genes), not a
> gene object.
> 
> Cheers,
> A
> 
> 
> On Tue, Sep 25, 2012 at 03:25:36PM +0100, Kieron Taylor wrote:
>> 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.
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
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>>>>> Ensembl Blog: http://www.ensembl.info/
>>>> 
>>>> Kieron Taylor PhD.
>>>> Ensembl Core software developer
>>>> 
>>>> EMBL - European Bioinformatics Institute
>>>> 
>> 
>> 
>> 
>> 
>> 
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>> 
> 
> -- 
> Andreas Kusalananda Kähäri
> Ensembl Gene Annotation Team
> 
> Sent from the tips of my fingers
> 
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