[ensembl-dev] retrive mouse and rat homologs

[Matthieu Muffato]

The error means that there is a typo in your script: you've used 
"fetch_by_registry_assembly()" instead of "fetch_by_registry_name()"

Cheers,
Matthieu

On 29/04/15 16:39, Jialin Liu wrote:
> Hi,
>
> I try to use fetch_by_registry_name, it's much better. However, I still got an mistake as below:
> Can't locate object method "fetch_by_registry_assembly" via package "Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor" at launch_akashi_all_orthologs_new.pl line 25.
>
> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
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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
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>
> --
> 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
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>

-- 
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