[ensembl-dev] HomologyAdaptor - function not working

[Javier Herrero]

Hi Marc

This is a good idea, however our API and database schema might be used 
by other people to store other data. In short, I am a bit reluctant on 
creating these hard links between the API and the data.

There are ways around it. For instance, we could rely on the 
method_link_type for this. We will consider implementing something in 
those lines.

Kind regards

Javier

On 19/04/12 08:47, Marc P. Hoeppner wrote:
> Hi,
>
> the members where genes, but the method_link_species_set was the EPO 
> 35 mammal alignment, which I am guessing wouldn't work in this 
> context? If so, maybe the API could throw something to alert the user 
> that the mlss must be of the type 'ENSEMBL_OTHOLOGUES' ?
>
> /Marc
>> Dear Marc
>>
>> I'm unfortunately not able to reproduce the bug.Here is my test code:
>>
>> my $mlss = 
>> $mlss_adaptor->fetch_by_method_link_type_registry_aliases('ENSEMBL_ORTHOLOGUES', 
>> ['human', 'mouse']);
>> my $member = 
>> $member_adaptor->fetch_by_source_stable_id("ENSEMBLGENE", 
>> "ENSG00000170037");
>> my $all_homologies = 
>> $homology_adaptor->fetch_all_by_Member_MethodLinkSpeciesSet($member, 
>> $mlss);
>>
>> $all_homologies contain 1 homology (with ENSMUSG00000032782)
>>
>> Can you provide an excerpt of the script you are running ?
>>
>> There are a few potential causes, can you please make sure that:
>>   - your member is a gene (not a peptide)
>>   - the method_link_type is ENSEMBL_ORTHOLOGUES (not ENSEMBL_HOMOLOGUES)
>>
>> Matthieu
>>
>> On 18/04/12 10:56, Marc P. Hoeppner wrote:
>>> Hi,
>>>
>>> I have been trying to get homologous genes to a human query using
>>>
>>> HomologyAdaptor::fetch_all_by_Member_MethodLinkSpeciesSet
>>>
>>> However, this returns an empty array, as far as I can tell. I have 
>>> tried
>>> it with the current version of the API and for different
>>> method_link_species_sets and member objects.
>>>
>>> Can anyone confirm that this is a bug, or does the problem exist on my
>>> end? The member object definitely has homologues, so that does not seem
>>> to be the problem.
>>>
>>> /Marc
>>>
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK