[ensembl-dev] HomologyAdaptor - function not working

Javier Herrero jherrero at ebi.ac.uk
Wed Apr 18 11:13:00 BST 2012

Hi Marc

It is likely that you are using a protein member instead of a gene 
member. The homologies are defined at the gene level although we use 
proteins in reality to get the gene trees.

We should probably support using protein members in the HomologyAdaptor, 
we will look into this for future releases of the API.

I hope this helps


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
> _______________________________________________
> 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/

Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

More information about the Dev mailing list