[ensembl-dev] retrieval of cosmic variant

Stef van Lieshout mailsvl at fastmail.fm
Wed Nov 16 15:07:16 GMT 2011


Ok, found it.

I was using "fetch_all_by_Slice" in the assumption this would return all
variations.

Instead one has to use "fetch_all_somatic_by_Slice" to get the
additional somatic variations.

I would seem logic to me if there would be specific methods
("fetch_somatic", "fetch_germline") to retrieve subsets and a general
"fetch_all" to retrieve all at once. Maybe an idea for the future..? ;)

Ciao,
Stef


----- Original message -----
From: "Stef van Lieshout" <mailsvl at fastmail.fm>
To: "Ensembl DevList" <dev at ensembl.org>
Date: Wed, 16 Nov 2011 15:51:16 +0100
Subject: retrieval of cosmic variant 

Hi,

I've been looking for this some time ago as well...but haven't found a
clear answer yet.

I want to find out whether a certain variation exists in COSMIC. For
this I can use the "fetch_Iterator_somatic": retrieving all, storing
them, and check for each of my variants whether this one is present in
the stored cosmic variants. But this isn't very efficient.

Isn't there a method I can use to directly check for a variationFeature
object if it is associated with a COSMIC id? When I retrieve all
variations for a 1 bp slice, I only seem to find CM##### ids (besides
rs###### ids) which do not seem to relate to the COSMIC "COSM#####"
ids...?

Thanks,
Stef





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