[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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