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

[Will McLaren]

Hi Ben,

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

http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1StrainSlice.html

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.

Cheers

Will

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
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/