[ensembl-dev] cosmic variants

Graham Ritchie grsr at ebi.ac.uk
Fri Jan 7 16:05:27 GMT 2011


Hi Stef,

These should be accessible via the API, they are stored in the database just like germline variations (though they are differentiated with the somatic column in the source table), how are you trying to access them? You might need to use specific somatic methods depending on how you are fetching object, e.g. VariationFeatureAdaptor::fetch_all_somatic_by_Slice instead of fetch_all_by_Slice, but you can also do e.g. VariationAdaptor::fetch_by_name('COSM492').

If you still can't find any then please forward on a code snippet and I'll take a look.

Cheers,

Graham


On 7 Jan 2011, at 15:30, mailsvl at fastmail.fm wrote:

> Hi,
> 
> Here's an example of cosmic info on the website:
> http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=11:533774-534774;v=COSM492;vdb=variation;vf=28419462
> 
> How to get to this info using the API? I can't find anything via
> variation objects or dblinks()..
> 
> -Stef
> __________________
> http://www.fastmail.fm
> 
> 
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