[ensembl-dev] HomologyAdaptor - function not working

[Matthieu Muffato]

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
>