def test_send_gene_request():
"""Test send request with correct params and endpoint"""
url = 'https://grch37.rest.ensembl.org/lookup/id/ENSG00000103591'
client = ensembl_api.EnsemblRestApiClient()
data = client.send_request(url)
# get info for the ensembl gene
assert data['display_name'] == 'AAGAB'
def liftover(build, chrom, start, end=None):
"""Perform variant liftover using Ensembl REST API
Accepts:
build(str): genome build: GRCh37 or GRCh38
chrom(str): 1-22,X,Y,MT
start(int): start coordinate
stop(int): stop coordinate or None
Returns
mappings(list of dict):
example: https://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json
"""
assembly2 = "GRCh38"
if build == "GRCh38":
assembly2 = "GRCh37"
client = ensembl_client.EnsemblRestApiClient()
url = "/".join(
[
client.server,
"map/human",
build,
f"{chrom}:{start}..{end or start}", # End variant provided is not required
f"{assembly2}?content-type=application/json",
]
)
result = client.send_request(url)
if isinstance(result, dict):
return result.get("mappings")
def test_send_request_wrong_url():
"""Successful requests are tested by other tests in this file.
This test will trigger errors instead.
"""
url = 'fakeyurl'
client = ensembl_api.EnsemblRestApiClient()
data = client.send_request(url)
assert type(data) == ValueError
url = 'https://grch37.rest.ensembl.org/fakeyurl'
data = client.send_request(url)
assert type(data) == HTTPError
def ensembl_to_symbol(ensembl_id):
"""Converts ensembl id to gene symbol
Accepts:
ensembl_id(str): an ensembl gene id. Ex: ENSG00000103591
Returns:
gene_symbol(str): an official gene symbol. Ex: AAGAB
"""
client = ensembl_client.EnsemblRestApiClient()
url = "".join([client.server, "/lookup/id/", ensembl_id])
results = client.send_request(url)
return results.get("display_name", None)
def test_except_on_invalid_response():
"""Test function that creates exception with message when response returned from Ensembl REST API has status code !=200"""
# GIVEN a response from Ensembl service with status != 200
client = ensembl_api.EnsemblRestApiClient()
class MockResponse:
def __init__(self):
self.status = 500
mockresp = MockResponse()
# Then it should trigger an exception
with pytest.raises(Exception):
result = client.except_on_invalid_response(mockresp)
def entrez_to_symbol(entrez_id):
"""Convert entrez id to gene symbol
Accepts:
entrez_id(str) ex. "3735"
Returns
gene_symbol(str) ex. BRAF
"""
client = ensembl_client.EnsemblRestApiClient()
url = "".join([
client.server, "/xrefs/name/human/", entrez_id,
"?external_db=EntrezGene"
])
results = client.send_request(url)
for gene in results: # result is an array. First element is enough
return gene["display_id"]
def symbol_to_ensembl(gene_symbol):
"""Convert gene symbol to ensembl id
Accepts:
gene_symbol(str) ex. LIMS2
Returns:
ensembl_id(str) ex. ENSG00000072163
"""
client = ensembl_client.EnsemblRestApiClient()
url = "".join([
client.server, "/xrefs/symbol/homo_sapiens/", gene_symbol,
"?external_db=HGNC"
])
results = client.send_request(url)
for gene in results: # result is an array. First element is enough
if gene["id"].startswith("ENSG"): # it's the ensembl id
return gene["id"]
def test_ping_ensemble_37():
"""Test ping ensembl server containing human build 37"""
client = ensembl_api.EnsemblRestApiClient()
data = client.ping_server()
assert data == {'ping': 1}
def test_ping_ensemble_38():
"""Test ping ensembl server containing human build 38"""
client = ensembl_api.EnsemblRestApiClient(build="38")
data = client.ping_server()
assert data == {"ping": 1}