[ensembl-dev] VEP Interpro ID & description

[Guillermo Marco Puche]

Ok I'm gonna give it a shot.
I installed latest API downloaded from Ensembl website on friday 
(10/05/2013) and I'm using a local Ensembl 71 database for VEP, no cache.

Best regards,
Guillermo

On 05/13/2013 01:45 PM, Will McLaren wrote:
> 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 
> <mailto: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
>>     <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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>>
>
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