[ensembl-dev] Problem using REST VEP endpoint on pig

Paolo Cozzi paolo.cozzi at itb.cnr.it
Tue Dec 9 21:12:11 GMT 2014


Dear Magali, Dear Will,

Thanks for your reply. Sorry I didn't see that Chromosome 21 make no 
sense for pig. The question rose up since in testing VEP endpoint I saw 
this error while the same query was successful (with no error and no 
results) on your previous version of REST server.

I think I will test my functions with appropriate data.

Thank you for you support,

regards,

Paolo.



Il 09/12/2014 17.05, Will McLaren ha scritto:
> Hi Paolo,
>
> The current Pig assembly does not have a chromosome 21:
>
> http://www.ensembl.org/Sus_scrofa/Location/Genome
>
> Of course, the error message you are seeing is not especially helpful; 
> we will look into a fix for this.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 5 December 2014 at 14:21, Paolo Cozzi <paolo.cozzi at itb.cnr.it 
> <mailto:paolo.cozzi at itb.cnr.it>> wrote:
>
>
>     Dear all,
>
>     Using the new release of REST - VEP endpoint, I got a 400 error
>     code for pig. More precisely, this is the command line I used:
>
>     $ curl -H "content-type:application/json" -H
>     "accept:application/json" --data '{ "variants" : ["21 26960070
>     <tel:21%2026960070> rs116645811 G A . . .", "21 26965148
>     <tel:21%2026965148> rs1135638 G A . . ." ] }'
>     http://rest.ensembl.org/vep/pig/region --verbose
>
>     And this is the result:
>
>     * About to connect() to rest.ensembl.org <http://rest.ensembl.org>
>     port 80 (#0)
>     *   Trying 193.62.52.232... connected
>     * Connected to rest.ensembl.org <http://rest.ensembl.org>
>     (193.62.52.232) port 80 (#0)
>     > POST /vep/pig/region HTTP/1.1
>     > User-Agent: curl/7.19.7 (x86_64-redhat-linux-gnu) libcurl/7.19.7
>     NSS/3.14.0.0 <http://3.14.0.0> zlib/1.2.3 libidn/1.18 libssh2/1.4.2
>     > Host: rest.ensembl.org <http://rest.ensembl.org>
>     > content-type:application/json
>     > accept:application/json
>     > Content-Length: 90
>     >
>     < HTTP/1.1 400 Bad Request
>     < Vary: Content-Type
>     < Content-Length: 168
>     < Content-Type: application/json
>     < X-Runtime: 0.141490
>     < X-RateLimit-Limit: 55000
>     < X-RateLimit-Reset: 2961
>     < X-RateLimit-Period: 3600
>     < X-RateLimit-Remaining: 54997
>     < Date: Fri, 05 Dec 2014 14:10:39 GMT
>     < Connection: close
>     <
>     * Closing connection #0
>     {"error":"Can't call method \"seq_region_Slice\" on an undefined
>     value at
>     /home/ensadmin/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
>     line 4223.\n"}
>
>     Thank you for your support,
>
>     Regards,
>
>     Paolo
>
>
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