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

[Michael Schuster]

On 29 Jun 2011, at 13:13, Susan Fairley wrote:

> Hi Sebastien,
>
> Yes, you do need to specify the database you want to connect to.
>
> It should be the database that the genes are stored in, also  
> specifying the dnadb if the sequence is stored elsewhere and you  
> want sequences.
>

In addition, the Bio::EnsEMBL::Registry->get_species_and_object_type()  
method allows to resolve an Ensembl stable identifier into the species  
name an even object type (i.e. Gene, Transcript), so exactly the  
information you need to connect an object adaptor to the correct  
database.

http://www.ensembl.org/info/docs/Pdoc/ensembl/modules/Bio/EnsEMBL/Registry.html#POD24

Best regards,
Michael


> Regards,
> Susan.
>
> Sébastien Moretti wrote:
>> Thanks for this alternative method.
>> Nevertheless it seems I still need a species name somewhere:
>> - with the -species argument
>> - or with the -dbname argument that, I guess, should be the species
>>  core database name.
>> Isn't it ?
>>> 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
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/