[ensembl-dev] REST server replies with "assembly_name":"GRCh38" with other species than human

Paolo Cozzi paolo.cozzi at itb.cnr.it
Tue Oct 14 16:25:38 BST 2014


Thank you for your timely reply,

I will check my scripts.

regards,

Paolo



Il 14/10/2014 17:14, mag ha scritto:
> Hi Paolo,
>
> Thanks for reporting this, it is nice to see the service is being used 
> and not just for human.
>
> The error has now been fixed, the two examples below should work fine.
>
>
> Regards,
> Magali
>
> On 14/10/2014 15:30, Paolo Cozzi wrote:
>>
>> Thank you all for your support, I'll check my scripts and I will 
>> control assembly detail.
>>
>> I have another bug to report: searching in VEP endpoint for sheep and 
>> horse, I got {"error":"something bad has happened"}. Here the curl 
>> lines:
>>
>> $ curl -H "content-type:application/json" -H 
>> "accept:application/json" --data '{ "variants" : ["21 26960070 
>> rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ] }' 
>> http://rest.ensembl.org/vep/sheep/region
>>
>> $ curl -H "content-type:application/json" -H 
>> "accept:application/json" --data '{ "variants" : ["21 26960070 
>> rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ] }' 
>> http://rest.ensembl.org/vep/horse/region
>>
>> Thank you for your sopport,
>>
>> regards,
>>
>> Paolo
>>
>>
>>
>> Il 14/10/2014 12:52, mag ha scritto:
>>> Hi Paolo,
>>>
>>> Thanks again for reporting this.
>>>
>>> The issue has been fixed and pushed onto our live server.
>>> Please do not hesitate to report any further issues.
>>>
>>>
>>> Regards,
>>> Magali
>>>
>>> On 13/10/2014 15:11, Paolo Cozzi wrote:
>>>>
>>>> Dear Kieron,
>>>>
>>>> thank you for your suggestion. I will temporarily fix my script in 
>>>> order to retrive the correct assembly via info endpoint. I will 
>>>> wait for VEP endpoint bugfix
>>>>
>>>> Regards,
>>>>
>>>> Paolo
>>>>
>>>>
>>>>
>>>> Il 13/10/2014 15:42, Kieron Taylor ha scritto:
>>>>> Hi Paolo,
>>>>>
>>>>> Thanks for your bug report. This is clearly an error. While the 
>>>>> VEP endpoint output may be reporting the wrong assembly, you can 
>>>>> still turn to info/assembly to get the correct response while we 
>>>>> figure out where the bug has come from.
>>>>>
>>>>> http://rest.ensembl.org/info/assembly/cow
>>>>>
>>>>> Regards,
>>>>>
>>>>> Kieron Taylor
>>>>> Ensembl Core
>>>>>
>>>>>
>>>>> On 13/10/2014 14:28, Paolo Cozzi wrote:
>>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> Using REST server with other species than human, I found always
>>>>>> "assembly_name":"GRCh38", for example:
>>>>>>
>>>>>> $ curl -H "content-type:application/json" -H 
>>>>>> "accept:application/json"
>>>>>> --data '{ "variants" : ["21 26960070 rs116645811 G A . . .", "21
>>>>>> 26965148 rs1135638 G A . . ." ] }' 
>>>>>> http://rest.ensembl.org/vep/cow/region
>>>>>>
>>>>>> [{"input":"21 26960070 rs116645811 G A . .
>>>>>> .","assembly_name":"GRCh38","end":26960070,"seq_region_name":"21","transcript_consequences":[{"gene_id":"ENSBTAG00000012351","variant_allele":"A","biotype":"protein_coding","gene_symbol_source":"EntrezGene","consequence_terms":["intron_variant"],"strand":1,"gene_symbol":"ARNT2","transcript_id":"ENSBTAT00000016391"}],"strand":1,"id":"rs116645811","allele_string":"G/A","most_severe_consequence":"intron_variant","start":26960070}, 
>>>>>>
>>>>>> ...
>>>>>>
>>>>>> Could be possible to fix assembly name?
>>>>>>
>>>>>> Thank you for your support,
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Paolo
>>>>>>
>>>>>>
>>>>>>
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>>>>>
>>>>>
>>>>>
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