[ensembl-dev] VEP Interpro ID & description

[Will McLaren]

There was a bug in --domains when using the cache that has been recently
fixed.

Try updating your API and see if that's any better.

Will


On 13 May 2013 12:38, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hello Will,
>
> Yes I'm currently running VEP with --domains flag. It always shown empty
> for the testings for different samples I've done until now.
> So domains flag is supposed to display the Interpro_ac for overlapping
> protein domains?
>
> Best regards,
> Guillermo.
>
>
> On 05/13/2013 01:34 PM, Will McLaren wrote:
>
> Hi Guillermo,
>
> Have you tried the --domains flag in the VEP?
>
>  Perhaps this is not enough information for you but it does provide the
> display label of overlapping protein domains.
>
>  The protein object is referred to as a translation object in the Ensembl
> API; you can retrieve it from the transcript via $transcript->translation.
>
>  See
> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html
>
>  Regards
>
>  Will
>
>
> On 13 May 2013 12:15, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>>  Hello,
>>
>> So it seems nobody has done this yet. I'll do it then :)
>>
>> Does VEP support any kind of """Proteinfeature"""? Checking the other
>> scripts it seems I must be using Transcript feature_type.
>>
>> Correct me if I'm wrong please, I'm a bit confused since interpro_ac is
>> part from Core ProteinFeature.  (EnsEMBL::ProteinFeature::interpro_ac)
>>
>> Best regards,
>> Guillermo.
>>
>>
>> On 05/09/2013 04:16 PM, Guillermo Marco Puche wrote:
>>
>>  Hello,
>>
>> Does anyone coded a plugin to obtain InterPro ID and description for VEP?
>> I've looked in VEP repo without luck.
>>
>> I want to know before start coding.
>>
>> Thank you !
>>
>> Best regards,
>> Guillermo.
>>
>>
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