[ensembl-dev] Ensembl REST API | link. diseq. using genomic range with other species?

Thu Jul 18 13:53:37 BST 2019

Thanks!

On Thu, 18 Jul 2019 at 13:38, Anja Thormann <anja at ebi.ac.uk> wrote:

> Hi Ramiro,
>
> we provide LD calculations for species for which we have sufficient amount
> of genotype data. Our script expects at least 40 samples per population for
> LD calculation. At the moment we have enough genotype data for human, goat
> and sheep.
>
> You can query our population endpoint for your species of interest  with
> the filter variable set to LD in order to find out for which populations LD
> can be calculated: For example for human:
>
> https://rest.ensembl.org/info/variation/populations/homo_sapiens?filter=LD;content-type=application/json
>
> We will provide better exception handling for the cases you have listed in
> your examples.
>
> Thank you,
> Anja
>
> On 18 Jul 2019, at 12:04, Ramiro Magno <ramiro.magno at gmail.com> wrote:
>
> Hi
>
> What should I expect when using this endpoint with other species than
> human:
>
> http://rest.ensembl.org/documentation/info/ld_region_get
>
> The returned errors do not seem to be consistent. Some expose internal
> errors even. I was expecting some error more specifically related to the
> invalid parameter.
>
> Here's some examples:
>
> *Example 1*
>
> * Endpoint:
> https://rest.ensembl.org/ld/gorilla/rs1042779/1000GENOMES:phase_3:CEU?window_size=50;d_prime=0;r2=0
> * Status code:    400
> * Error message: "Can't call method "max_snp_distance" on an undefined
> value at
> /nfs/public/release/ensweb/live/rest/www_97/ensembl-rest/lib/EnsEMBL/REST/Model/LDFeatureContainer.pm
> line 50.
>
> *Example 2*
>
> * Endpoint:
> https://rest.ensembl.org/ld/gorilla/region/1:1..10000/1000GENOMES:phase_3:CEU?d_prime=0;r2=0
> * Status code:    400
> * Error message: "Can't call method "db" on an undefined value at
> /nfs/public/release/ensweb/live/rest/www_97/ensembl-rest/lib/EnsEMBL/REST/Model/LDFeatureContainer.pm
> line 92.
>
> *Example 3*
>
> * Endpoint:
> https://rest.ensembl.org/ld/fly/region/1:1..10000/1000GENOMES:phase_3:CEU?d_prime=0;r2=0
> * Status code: 500
> * Error message:  Error: lexical error: invalid char in json text.
>                                        <!DOCTYPE html>    <html lang="
>                      (right here) ------^
>
> Cheers,
> RM
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