[ensembl-dev] Sus scrofa is not a valid species name?

Alexander Pico apico at gladstone.ucsf.edu
Thu Jun 21 20:10:19 BST 2012

Thanks Dan,

I've been dealing with bacteria collections for a while using this approach,
but it's no longer working for me:

my $gene_adaptor = $registry->get_adaptor($species, "core", "gene");

Where $species is "escherichia_coli". I've tried these as well:
 * escherichia_collection
 * "Escherichia coli"
 * escherichia_shigella_collection

I can confirm the following local database is available by:
    my @db_adaptors = @{ $registry->get_all_DBAdaptors() };

Printing $db_adaptor->dbc()->dbname(), ->species(), and ->group() provides:

database    escherichia_collection_core_14_67_5
species/group    e_coli_se11/core
species/group    e_coli_o127_h6/core
species/group    e_coli_o17_k52_h18/core
species/group    e_fergusonii/core
species/group    e_coli_55989/core
species/group    e_coli_o8/core
species/group    e_coli_o45_k1/core
species/group    e_coli_o81/core
species/group    e_coli_o7_k1/core
species/group    e_coli_bw2952/core
species/group    e_coli_bl21/core
species/group    e_coli_rel606/core
species/group    e_coli_tw14359/core
species/group    e_coli_o26_h11/core
species/group    e_coli_o103_h2/core
species/group    e_coli_o111_h_/core
species/group    e_coli_bl21_de3_kribb/core
species/group    e_coli_atcc_33849/core
species/group    e_coli_bl21_de3_jgi/core
species/group    s_flexneri_x/core
species/group    e_coli_se15/core
species/group    e_coli_042/core
species/group    e_coli_o55_h7/core
species/group    e_coli_o157_h7_tw14588/core
species/group    e_coli_o18_k1_h7/core

Do I have to pick one of these now?  Does anyone know which one corresponds
to "regular" E.coli or the default one that used to be loaded?

 - Alex

On 6/20/12 11:22 PM, "Dan Staines" <dstaines at ebi.ac.uk> wrote:

> On 06/21/2012 12:42 AM, Alexander Pico wrote:
>> Great. That worked for pig. But I¹m now stuck on the bacteria
>> collections, specifically:
>> escherichia_shigella_collection
>> bacillus_collection
>> mycobacterium_collection
>> I¹ve tried the above, plus Œescherichia_coli¹ (which used to work) and
>> ŒEscherichia coli¹.  Any suggestions for these species in v67?
> Bacteria are handled by Ensembl in a different way to other species, so
> just to be clear - can you let us know a bit more about what you're
> trying to achieve, preferably with a bit of example Perl code?
> Cheers,
> Dan.

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