Extracting GTEX Data using GTEX portal API

Question

I am trying to extract gtex eqtl data from GtexPortal using their API : https://gtexportal.org/home/apiPage

I am looking to extract data for a given SNP ID and tissue location.

I am new to coding and python so I am not sure if what I am doing is right but an example of code I have tried where I give a specific Gene, tissue, and variant ID and am looking to extract the data for these paramaters from the indepndentEqtl data of gtexportal:

gencode = "ENSG00000122971"
gene_name = "ALMS1"
tissue = "Heart_Left_Ventricle"

gene_eqtls = requests.get('https://gtexportal.org/api/v2/association/independentEqtl', params = {"gencodeId" : gencode,"tissueSiteDetailId" : tissue, "datasetId" : "gtex_v8", "variantId" : 'rs58235352'})

data = json.loads(gene_eqtls.text)
data

{'data': [],
 'paging_info': {'numberOfPages': 0,
  'page': 0,
  'maxItem
sPerPage': 250,
  'totalNumberOfItems': 0}}

Everything I have been trying has been giving these empty data sets and any help in extracting the data would be greatly appreciated.

Answer 1

the gencodeId needs to be versioned, as per GTEx API docs (e.g. ENSG00000122971.9, see ensembl).

However, I also think there is no output for your example gene in this case anyway. Compare with the following example, which does return some results for me:

import requests
import json

json.loads(requests.get('https://gtexportal.org/api/v2/association/independentEqtl', params = {"gencodeId" : "ENSG00000122971.9", "datasetId" : "gtex_v8"}).text)