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

Thu Jul 18 13:37:52 BST 2019

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 <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 <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 <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 <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 <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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