[ensembl-dev] Variation - apply variant to slice and return it

Will McLaren wm2 at ebi.ac.uk
Thu Jul 5 14:18:43 BST 2012

Hi Ben,

You might be able to do something with the StrainSlice code.


This is essentially a slice with an associated list of variation
feature objects.

When you call $strain_slice->seq, the variant sequences are applied to
the slice's sequence and the changed sequence returned.

You'd have to spoof creating one; take a look at the new method in the
above, and the seq method for how it applies the sequence changes.



On 5 July 2012 14:12, Benoît Ballester <benoit.ballester at inserm.fr> wrote:
> Hi Dev,
> I'd like to know if it is possible to get the sequence (slice) with a given variant on it.
> Eg: Let say this sequence AGAG as a variant G>T at +2, then the API will return ATAG.
> Is this possible with the Ensembl API ?
> I hope I made myself clear ?
> Thanks,
> Ben
> --
> Benoît Ballester, PhD
> Inserm U1090, TAGC
> Marseille - France
> +33 4 91 82 87 39
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