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

[mag]

Hi Simon,

For ensembl genomes species, we recommend using the LookUp method as 
described here:
http://bacteria.ensembl.org/info/data/accessing_ensembl_bacteria.html#intro

For a given registry, you can use the 'get_all_by_name_pattern' method 
for approximate matching.

my $lookup = Bio::EnsEMBL::LookUp->new(-URL=>"http://bacteria.ensembl.org/registry.json",-NO_CACHE=>1);
my @dbas = @{$lookup->get_all_by_name_pattern('escherichia_coli_.*')};

or by taxon id

my @dbas = @{$lookup->get_all_by_taxon_id(388919)};

If it still fails to find the species you are looking for, I would try 
running the ping_ensembl.pl script to make sure you are connecting to 
the right databases.


Regards,
Magali

On 24/02/2014 12:03, Simon Andrews wrote:
> 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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