[ensembl-dev] retrieval of cosmic variant

[Fiona Cunningham]

Dear Stef,

Many thanks for answering your own question on dev ;-)

Thank you for your suggestions as well to have additional specific
calls for germline and somatic variants. We did consider these of
course but it is more important to maintain backwards compatibility of
the existing methods and so we did not change the functionality of the
current methods. Germline and somatic variation are really very
different biological processes and so we decided it was better not to
confound the two in a 'fetch_all' method either.

I hope you found the documentation on this good enough. Do let us know
if you have any further suggestions.

Best wishes,

Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612



On 16 November 2011 15:07, Stef van Lieshout <mailsvl at fastmail.fm> wrote:
> 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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