[ensembl-dev] [Compara] V. 59: GenomeDB->name now returns names in different format

Andy Yates ayates at ebi.ac.uk
Fri Aug 27 17:18:01 BST 2010


Hi Giuseppe,

This is a change that is here to stay and has been done to tighten up the link between an ensembl core database & it's entry in the compara genome_db table. The value in genome_db is the same as the meta value 'species.production_name' in the core database. A lot of work was carried out in the code to create a compute friendly value from a species name which is fine for species like Human but breaks down once we look at strains especially when they can contain characters like : or / and \ in their name. 

if you want the full name of a GenomeDB either consult the taxonomy or go back to the core database from the GenomeDB object (using the db_adaptor() call). To go the other way hand GenomeDBAdaptor a core DBAdaptor and it will do the necessary lookups to find the right GenomeDB.

Regards,`

Andy

On 27 Aug 2010, at 17:05, Giuseppe Gallone wrote:

> Hi,
> 
> I just installed the API V.59 and found out that now a call to GenomeDB->name will return species names in the
> 
> homo_sapiens
> 
> format, rather than
> 
> Homo sapiens
> 
> format, like before. Is this a change that's here to stay or do you plan to review it? Just asking because I had some code checking all the genomes by the full name. Should I check the genomes by the NCBI taxon id instead (maybe more likely not to change)?
> 
> Thanks
> Giuseppe
> 
> 
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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/








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