[ensembl-dev] retrive mouse and rat homologs

[Jialin Liu]

Hi Matthieu,

Many thanks for you nice reply.
I querying the live database.
And my set up of registry like this:
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db(
 -host=>"ensembldb.ensembl.org",
 -user=>"anonymous"
 );

Jialin    
________________________________________
From: dev-bounces at ensembl.org <dev-bounces at ensembl.org> on behalf of Matthieu Muffato <muffato at ebi.ac.uk>
Sent: Wednesday, April 29, 2015 4:57 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] retrive mouse and rat homologs

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
Fax   + 44 (0) 1223 49 4468

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