[ensembl-dev] retrive mouse and rat homologs

[Jialin Liu]

Thanks a lot. Got it.

Cheers,
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 5:24 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] retrive mouse and rat homologs

Right: you are using fetch_by_name_assembly() which requires the exact
"production name" used for that species (usually the scientific name
with underscores but I think there are exceptions).

The safest is to use instead fetch_by_registry_name() which takes any of
the names that are defined in the database, e.g. "mouse", "mmus",
"m_musculus", "Mus musculus", etc

Matthieu

On 29/04/15 16:06, Jialin Liu wrote:
> 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";
> $reg->load_registry_from_db(
>   -host=>"ensembldb.ensembl.org",
>   -user=>"anonymous"
>   );
>
> Jialin
> ________________________________________
> From: dev-bounces at ensembl.org <dev-bounces at ensembl.org> on behalf of Matthieu Muffato <muffato at ebi.ac.uk>
> Sent: Wednesday, April 29, 2015 4:57 PM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] retrive mouse and rat homologsfetch_by_name_assembly
>
> Dear Jialin,
>
> Are you querying the live database or your own copy ?
> How are you setting up the Registry ?
>
> Matthieu
>
> On 29/04/15 15:45, Jialin Liu wrote:
>> Dear list
>>
>>
>> I want to retrive mouse and rat homologs, using script as below.
>> However, I get mistake like this:
>>
>>
>>      MSG: No matches found for name 'Mus musculus' and assembly '--undef--'
>>
>>      STACK Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor::fetch_by_name_assembly
>>      /Users/jliu5/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL
>>
>>      /GenomeDBAdaptor.pm:108
>>
>>
>> I am wondering are there some adaptors or fetch methods ace changed?
>>
>>
>>      my script:
>>
>>      my$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
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
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> _______________________________________________
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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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