[ensembl-dev] retrive mouse and rat homologs

[Jialin Liu]

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 @orthologies = @{$homology_adaptor->fetch_all_by_MethodLinkSpeciesSet

($mlss_orth)};


Any ideas?

Cheers,

Jialin

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