Module ieugwaspy.query
API query functions
Expand source code
"""API query functions
"""
import ieugwaspy.constants as cons
import ieugwaspy.variants as variants
import ieugwaspy.backwards as backwards
import json, requests, os
def api_query(path, query="", method="GET", access_token=cons.api_token):
"""This is a general-purpose function called by other functions to query the API and return the resulting data in JSON format.
Parameters:
path: the path component of the URL
query: any query to go after the ?query component of the URL
access_token: the OAuth access token
Returns:
data: json object as returned by API
""" # Still need to handle timeouts
ntry = 0
ntries = 3
if method == "GET":
if query != "":
url = "{}{}?query={}&access_token={}".format(
cons.option["mrbaseapi"], path, query, access_token
)
else:
url = "{}{}?access_token={}".format(
cons.option["mrbaseapi"], path, access_token
)
print(url)
response = requests.get(url)
elif method == "POST":
url = "{}{}".format(cons.option["mrbaseapi"], path)
response = requests.post(url, data=query)
else:
return "Invalid API method"
data = json.loads(response.text)
return data
def api_status():
"""Check API status
Returns:
data: API status
"""
data = api_query("status")
return data
def gwasinfo(id="", access_token=cons.api_token):
"""This function will return GWAS study meta-data describing the specific studies selected by id
Parameters:
id: ID(s) of specific studies (Python list)
access_token: the OAuth access token
Returns:
data: json object as returned by API
"""
id = ",".join(id)
if id != "":
data = api_query("gwasinfo/{}".format(id), access_token=access_token)
else:
data = api_query("gwasinfo/list", access_token=access_token)
return data
def associations(
variantlist,
id,
proxies=1,
r2=0.8,
align_alleles=1,
palindromes=1,
maf_threshold=0.3,
access_token=cons.api_token,
):
"""Retrieve associations for specific SNP/study combinations
Parameters:
variantlist: list of variants (Python list)
id: list of study IDs (Python list)
proxies: proxies 0 or (default) 1 - indicating whether to look for proxies
r2: minimum proxy LD rsq value. Default=0.8
align_alleles: try to align tag alleles to target alleles (if proxies = 1). 1 = yes (default), 0 = no
palindromes: allow palindromic SNPs (if proxies = 1). 1 = yes (default), 0 = no
maf_threshold: MAF threshold to try to infer palindromic SNPs. Default = 0.3.
access_token: the OAuth access token
Returns:
data: json object as returned by API
"""
id = backwards.legacy_ids(id)
data = {
"variant": variantlist,
"id": id,
"proxies": proxies,
"r2": r2,
"align_alleles": align_alleles,
"palindromes": palindromes,
"maf_threshold": maf_threshold,
"access_token": access_token,
}
result = api_query("associations", query=data, method="POST")
return result
def phewas(variantlist, pval=1e-3, access_token=cons.api_token):
"""Perform phenome-wide association analysis (PheWAS) of variant(s) across all traits in the IEU GWAS database
Parameters:
variants: list of variants (Python list)
pval: p-value threshold
access_token: the OAuth access token
Returns:
data: json object as returned by API
"""
rsid = ",".join(variants.variants_to_rsid(variantlist))
data = api_query("phewas/{}/{}".format(rsid, pval), access_token=access_token)
return data
def tophits(
id,
pval=5e-8,
clump=1,
r2=0.001,
kb=10000,
force_server=False,
access_token=cons.api_token,
):
"""Retrieve association data for specific SNP/study combinations
Parameters:
id: list of study IDs (Python list)
pval: use this p-value threshold. Default = 5e-8
clump: whether to clump (1) or not (0). Default = 1
r2: use this clumping r2 threshold. Default is very strict, 0.001
kb: use this clumping kb window. Default is very strict, 10000
force_server: True/False. By default (False) will return preclumped hits. p-value threshold 5e-8, with r2 threshold 0.001 and kb threshold 10000, using only SNPs with MAF > 0.01 in the European samples in 1000 genomes. If force_server = TRUE then will recompute using server side LD reference panel.
access_token: the OAuth access token
Returns:
data: json object as returned by API
"""
id = backwards.legacy_ids(id)
if clump == 1 and r2 == 0.001 and kb == 10000 and pval == 5e-8:
preclumped = 1
else:
preclumped = 0
if preclumped == 1 and force_server:
preclumped = 0
data = {
"id": id,
"pval": pval,
"preclumped": preclumped,
"clump": clump,
"r2": r2,
"kb": kb,
"access_token": access_token,
}
result = api_query("tophits", query=data, method="POST")
return resultFunctions
def api_query(path, query='', method='GET', access_token='NULL')-
This is a general-purpose function called by other functions to query the API and return the resulting data in JSON format.
Parameters
path- the path component of the URL
query- any query to go after the ?query component of the URL
access_token- the OAuth access token
Returns
data- json object as returned by API
Expand source code
def api_query(path, query="", method="GET", access_token=cons.api_token): """This is a general-purpose function called by other functions to query the API and return the resulting data in JSON format. Parameters: path: the path component of the URL query: any query to go after the ?query component of the URL access_token: the OAuth access token Returns: data: json object as returned by API """ # Still need to handle timeouts ntry = 0 ntries = 3 if method == "GET": if query != "": url = "{}{}?query={}&access_token={}".format( cons.option["mrbaseapi"], path, query, access_token ) else: url = "{}{}?access_token={}".format( cons.option["mrbaseapi"], path, access_token ) print(url) response = requests.get(url) elif method == "POST": url = "{}{}".format(cons.option["mrbaseapi"], path) response = requests.post(url, data=query) else: return "Invalid API method" data = json.loads(response.text) return data def api_status()-
Check API status
Returns
data- API status
Expand source code
def api_status(): """Check API status Returns: data: API status """ data = api_query("status") return data def associations(variantlist, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold=0.3, access_token='NULL')-
Retrieve associations for specific SNP/study combinations
Parameters
variantlist- list of variants (Python list)
id- list of study IDs (Python list)
proxies- proxies 0 or (default) 1 - indicating whether to look for proxies
r2- minimum proxy LD rsq value. Default=0.8
align_alleles- try to align tag alleles to target alleles (if proxies = 1). 1 = yes (default), 0 = no
palindromes- allow palindromic SNPs (if proxies = 1). 1 = yes (default), 0 = no
maf_threshold- MAF threshold to try to infer palindromic SNPs. Default = 0.3.
access_token- the OAuth access token
Returns
data- json object as returned by API
Expand source code
def associations( variantlist, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold=0.3, access_token=cons.api_token, ): """Retrieve associations for specific SNP/study combinations Parameters: variantlist: list of variants (Python list) id: list of study IDs (Python list) proxies: proxies 0 or (default) 1 - indicating whether to look for proxies r2: minimum proxy LD rsq value. Default=0.8 align_alleles: try to align tag alleles to target alleles (if proxies = 1). 1 = yes (default), 0 = no palindromes: allow palindromic SNPs (if proxies = 1). 1 = yes (default), 0 = no maf_threshold: MAF threshold to try to infer palindromic SNPs. Default = 0.3. access_token: the OAuth access token Returns: data: json object as returned by API """ id = backwards.legacy_ids(id) data = { "variant": variantlist, "id": id, "proxies": proxies, "r2": r2, "align_alleles": align_alleles, "palindromes": palindromes, "maf_threshold": maf_threshold, "access_token": access_token, } result = api_query("associations", query=data, method="POST") return result def gwasinfo(id='', access_token='NULL')-
This function will return GWAS study meta-data describing the specific studies selected by id
Parameters
id- ID(s) of specific studies (Python list)
access_token- the OAuth access token
Returns
data- json object as returned by API
Expand source code
def gwasinfo(id="", access_token=cons.api_token): """This function will return GWAS study meta-data describing the specific studies selected by id Parameters: id: ID(s) of specific studies (Python list) access_token: the OAuth access token Returns: data: json object as returned by API """ id = ",".join(id) if id != "": data = api_query("gwasinfo/{}".format(id), access_token=access_token) else: data = api_query("gwasinfo/list", access_token=access_token) return data def phewas(variantlist, pval=0.001, access_token='NULL')-
Perform phenome-wide association analysis (PheWAS) of variant(s) across all traits in the IEU GWAS database
Parameters
variants- list of variants (Python list)
pval- p-value threshold
access_token- the OAuth access token
Returns
data- json object as returned by API
Expand source code
def phewas(variantlist, pval=1e-3, access_token=cons.api_token): """Perform phenome-wide association analysis (PheWAS) of variant(s) across all traits in the IEU GWAS database Parameters: variants: list of variants (Python list) pval: p-value threshold access_token: the OAuth access token Returns: data: json object as returned by API """ rsid = ",".join(variants.variants_to_rsid(variantlist)) data = api_query("phewas/{}/{}".format(rsid, pval), access_token=access_token) return data def tophits(id, pval=5e-08, clump=1, r2=0.001, kb=10000, force_server=False, access_token='NULL')-
Retrieve association data for specific SNP/study combinations
Parameters
id- list of study IDs (Python list)
pval- use this p-value threshold. Default = 5e-8
clump- whether to clump (1) or not (0). Default = 1
r2- use this clumping r2 threshold. Default is very strict, 0.001
kb- use this clumping kb window. Default is very strict, 10000
force_server- True/False. By default (False) will return preclumped hits. p-value threshold 5e-8, with r2 threshold 0.001 and kb threshold 10000, using only SNPs with MAF > 0.01 in the European samples in 1000 genomes. If force_server = TRUE then will recompute using server side LD reference panel.
access_token- the OAuth access token
Returns
data- json object as returned by API
Expand source code
def tophits( id, pval=5e-8, clump=1, r2=0.001, kb=10000, force_server=False, access_token=cons.api_token, ): """Retrieve association data for specific SNP/study combinations Parameters: id: list of study IDs (Python list) pval: use this p-value threshold. Default = 5e-8 clump: whether to clump (1) or not (0). Default = 1 r2: use this clumping r2 threshold. Default is very strict, 0.001 kb: use this clumping kb window. Default is very strict, 10000 force_server: True/False. By default (False) will return preclumped hits. p-value threshold 5e-8, with r2 threshold 0.001 and kb threshold 10000, using only SNPs with MAF > 0.01 in the European samples in 1000 genomes. If force_server = TRUE then will recompute using server side LD reference panel. access_token: the OAuth access token Returns: data: json object as returned by API """ id = backwards.legacy_ids(id) if clump == 1 and r2 == 0.001 and kb == 10000 and pval == 5e-8: preclumped = 1 else: preclumped = 0 if preclumped == 1 and force_server: preclumped = 0 data = { "id": id, "pval": pval, "preclumped": preclumped, "clump": clump, "r2": r2, "kb": kb, "access_token": access_token, } result = api_query("tophits", query=data, method="POST") return result