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

[Alexander Pico]

Ah, I found "Escherichia coli K12" works. Now I have to find the secret
names of the other bacteria I want. Are these adaptor species names listed
anywhere?

 - Alex



On 6/21/12 12:10 PM, "Alexander Pico" <apico at gladstone.ucsf.edu> wrote:

> 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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