[ensembl-dev] VEP Interpro ID & description

[Guillermo Marco Puche]

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 
> <mailto: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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