[ensembl-dev] VEP Interpro ID & description
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Mon May 13 12:49:49 BST 2013
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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