[ensembl-dev] Gene adaptor when the species is unknown]

[Sébastien Moretti]

Thanks Ian & Michael

I didn't know this method and it does exactly what I need.

I only have stable_ids.
So, do you think it is a good idea to force $object_type and $db_type to 
be respectively 'Core' and 'Gene' directly ?



> If you know the stable_id of the gene you could try
>
> get_species_and_object_type
>
> i.e.
> my $stable_id = 'ENST00000326632';
>
>                  my ( $species, $object_type, $db_type ) =
>                    $registry->get_species_and_object_type($stable_id);
>
>                  my $adaptor =
>                    $registry->get_adaptor( $species, $db_type,
>                                            $object_type );
>
>                  my $object = $adaptor->fetch_by_stable_id($stable_id);
>
>
> If you just have a common gene name like "BRCA2" then you would need
> to loop over all the gene adaptors and and try fetch
>
> @genes = @{$gene_adaptor->fetch_all_by_external_name('BRCA2')}
>
>
> -Ian
> Ensembl Developer
>
> On Wed, Jun 29, 2011 at 12:44 PM, Susan Fairley<sf7 at sanger.ac.uk>  wrote:
>> Hi Sebastien,
>>
>> If you have a DBAdaptor you can then get a gene adaptor without
>> mentioning the species.
>>
>> my $genedb = new Bio::EnsEMBL::DBSQL::DBAdaptor( -host   =>  $gene_host,
>>                                              -user   =>  $gene_user,
>>                                              -pass   =>  $gene_pass,
>>                                              -port   =>  $gene_port,
>>                                              -dbname =>  $gene_dbname);
>>
>>
>> my $ga = $genedb->get_GeneAdaptor();
>>
>> Hope this helps.
>>
>> Regards,
>> Susan.
>>
>>
>> Sébastien Moretti wrote:
>>>
>>> Hi,
>>> I wonder if there is another way to create a gene adaptor.
>>> I use that but it is linked to a particular species:
>>>      my $gene_adaptor = $reg->get_adaptor( 'Human', 'Core', 'Gene' );
>>>
>>>
>>> I would like to get information about genes from ensembl gene identifiers
>>> (stable_id) without knowing a priori the species.
>>> I.e. what I have to put in the 'Human' place.
>>>
>>>
>>> So, is there something more generic to create gene adaptor ?
>>>
>>> Best regards

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://bioinfo.unil.ch/