[ensembl-dev] $NCBI_taxon_adaptor->fetch_node_by_name() broken in EnsemblGenomes 7

[Andy Yates]

Hi Giuseppe,

It seems that the taxonomy tables were missed out of the load for some unknown reason. I have gone & populated the servers and am updating the MySQL dumps we provide so for anyone who is providing mirrors of this data you will have to update ncbi_taxa_name and ncbi_taxa_node.

Your method should now work. However as an aside if you are looking for homologies linked to Plasmodium falciparum please watch out for the naming used in the Taxonomy as well as the taxonomy identifier linked to the genome db. In this situation our falciparum is linked to taxon 36329 which has the name Plasmodium falciparum 3D7. Using Plasmodium falciparum will return back 5833 & will not link to any valid GenomeDB.

Reagrds,

Andy

On 14 Dec 2010, at 13:16, Giuseppe G. wrote:

> Hi,
> 
> There is a problem with $NCBI_taxon_adaptor->fetch_node_by_name() in release 60.
> 
> 
> STEPS TO REPRODUCE THE BUG
> --------------------------
> 
> 1) get a registry by doing
>          $registry->load_registry_from_multiple_dbs(
>          {    #VERTEBRATES
>                  -host       => 'ensembldb.ensembl.org',
>                  -user       => 'anonymous',
>                  -verbose    => 1
>              },
>          {     #EnsemblGenomes
>                     -host    => 'mysql.ebi.ac.uk',
>                     -user    => 'anonymous',
>                     -port    => 4157,
>                     -verbose => 1
>              }
>          );
> 
> -this step is successful
> 
> 2) get a taxon adaptor using pan_homology by doing
> 
> my $NCBI_taxon_adaptor = $registry->get_adaptor('pan_homology', 'compara', "NCBITaxon");
> 
> -this step is successful
> 
> 3) get a taxon id from the species name by using fetch_node_by_name()
> 
> my $source_taxon = $NCBI_taxon_adaptor->fetch_node_by_name($source_organism);
> 
> where for $source_organism I tried 'Plasmodium falciparum', 'plasmodium_falciparum', 'drosophila_melanogaster', ecc ecc
> 
> -source_taxon is undefined
> -----------------------------
> 
> 
> ADDITIONAL INFORMATION
> ----------------------
> -This worked  in release 59/6
> -The method still works when the registry is connecting to vertebrate compara
> 
> 
> Any help is particularly appreciated because a core feature of my scripts relies on this adaptor and its seamless functionality (as per API docs) across Multi, ensemblgenomes and pan compara.
> 
> 
> Thanks a lot in advance.
> 
> Giuseppe
> 
> 
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> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/