[ensembl-dev] HomologyAdaptor - function not working

Marc P. Hoeppner mphoeppner at gmail.com
Thu Apr 19 08:47:06 BST 2012


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' ?

> 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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