[ensembl-dev] Structure of species names for slice adapters

Simon Andrews simon.andrews at babraham.ac.uk
Mon Feb 24 12:03:34 GMT 2014


I have a script which used to go through all possible adapters in the registry to give me a choice of genomes to process.  However in recent ensemblgenomes releases this no longer works as it takes so long to get through the thousands of adapters that it never completes.

I'm therefore trying to set up a specific slice adapter for the species I want.  The problem is I can't find the correct name to use and I don't know how to get it.  I'm trying to work with the latest S pombe release and my adapter setup looks like this:

$slice_adapter = $registry->get_adaptor($species,'Core','Slice');

..I've tried various things in $species "S pombe" "Schizosaccharomyces pombe" "yeast" and probably some others, but all of them return MSG: S pombe is not a valid species name (check DB and API version).

How do I find the correct name to use for any given species?

Thanks

Simon.
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