[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
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