[ensembl-dev] retrive mouse and rat homologs

[Matthieu Muffato]

Dear Jialin,

Are you querying the live database or your own copy ?
How are you setting up the Registry ?

Matthieu

On 29/04/15 15:45, Jialin Liu wrote:
> Dear list
>
>
> I want to retrive mouse and rat homologs, using script as below.
> However, I get mistake like this:
>
>
>     MSG: No matches found for name 'Mus musculus' and assembly '--undef--'
>
>     STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly
>     /Users/jliu5/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL
>
>     /GenomeDBAdaptor.pm:108
>
>
> I am wondering are there some adaptors or fetch methods ace changed?
>
>
>     my script:
>
>     my$homology_adaptor= $reg->get_adaptor("Multi", "compara", "Homology");
>
>     my$mlss_adaptor= $reg->get_adaptor("Multi", "compara",
>     "MethodLinkSpeciesSet");
>
>     my$genomedb_adaptor= $reg->get_adaptor("Multi", "compara", "GenomeDB");
>
>     my$sp1_gdb= $genomedb_adaptor->fetch_by_name_assembly("Mus musculus");
>
>     my$sp2_gdb= $genomedb_adaptor->fetch_by_name_assembly("Rattus
>     norvegicus");
>
>     my$mlss_orth= $mlss_adaptor- > fetch_by_method_link_type_GenomeDBs
>
>     ('ENSEMBL_ORTHOLOGUES', [$sp1_gdb, $sp2_gdb]);
>
>     my at orthologies= @{$homology_adaptor->fetch_all_by_MethodLinkSpeciesSet
>
>     ($mlss_orth)};
>
>
> Any ideas?
>
> Cheers,
>
> Jialin
>
>
>
>
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-- 
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
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