[ensembl-dev] VEP Rest API very slow

[Sarah Hunt]

Hi Beat,

We have updated the reference data our e!93 REST service is using, so it 
is now operating at normal speed.

Best wishes,

Sarah


On 20/07/2018 08:02, Sarah Hunt wrote:
>
> Hi Beat,
>
> Don't worry about changing your code. We have established that the 
> problem is due to a lack of indexing on some of the reference data VEP 
> is using. We will fix this as soon as possible.
>
> If you need to use the service right now, the reference files 
> containing both Ensembl and RefSeq transcripts are indexed, so it 
> would be quicker to use a request like this:
>
> https://rest.ensembl.org/vep/hsapiens/id/rs539044217?merged=1&content-type=application/json 
>
>
> Apologies for the inconvenience.
>
> Best wishes,
>
> Sarah
>
>
> On 19/07/2018 17:15, Wolf Beat wrote:
>> Dear Sarah,
>>
>>
>> Thank you for the fast answer. As there are incompatible changes 
>> between e93 and e92, notably in the VEP endpoint, moving back to e93 
>> now that the my code has changed, is not ideal.
>>
>> What is the plan for the VEP backend, will it be broken for the 
>> forseable future (which means i need to revert my code changes and do 
>> some other changes), or is it a matter of days, in which case i can 
>> avoid changing my code?
>>
>>
>> Kind regards
>>
>>
>> Beat Wolf
>>
>> ________________________________
>> From: Dev <dev-bounces at ensembl.org> on behalf of Sarah Hunt 
>> <seh at ebi.ac.uk>
>> Sent: Thursday, July 19, 2018 5:41:13 PM
>> To: Ensembl developers list
>> Subject: Re: [ensembl-dev] VEP Rest API very slow
>>
>>
>> Hi Beat,
>>
>> We are looking into this, but in the meantime, the archive of our e!92
>> release is available here:  http://wp-p1m-6e.ebi.ac.uk:5000
>>
>> It should be available as: http://e92.rest.ensembl.org/ shortly.
>>
>> Sarah
>>
>> On 19/07/2018 16:08, Wolf Beat wrote:
>>> Hello,
>>>
>>>
>>> i was wondering why the ensembl VEP rest API is very slow.
>>>
>>> When i try for example this query:
>>>
>>> http://rest.ensembl.org/vep/hsapiens/id/rs539044217?content-type=application/json<http://rest.ensembl.org/vep/hsapiens/id/rs539044217?distance=-100000&content-type=application/json> 
>>>
>>>
>>>
>>> It takes up to 10 seconds.
>>>
>>> It seems like the issue is not related to the actual VEP work 
>>> (effect prediction), because if i add the following parameter:
>>>
>>> http://rest.ensembl.org/vep/hsapiens/id/rs539044217?distance=-100000&content-type=application/json 
>>>
>>>
>>>
>>> thus removing basically all genes from the prediction, it takes an 
>>> equal amount of time.
>>>
>>>
>>> This is quite an urgent issue for me. Is there a faster way to 
>>> retrieve frequences (ok that one i know) AND polyphen/sift 
>>> predictions in the same query, that is faster?
>>>
>>>
>>> Kind regards
>>>
>>>
>>> Beat Wolf
>>>
>>>
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>