def test_multi_insertion():
"""Find a variantTypes INS at a position where there are two different variants."""
query = dict(QUERY)
query['start'] = 16879600
query['end'] = 16879601
query['referenceBases'] = 'T'
del query['alternateBases']
query['variantType'] = 'INS'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 116,
"sampleCount": 2504,
"exists": True,
"referenceBases": "T",
"alternateBases": "TAA",
"variantType": "INS",
"frequency": 0.023162939,
}
gold2 = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 314,
"sampleCount": 2504,
"exists": True,
"referenceBases": "T",
"alternateBases": "TA",
"variantType": "INS",
"frequency": 0.062699683,
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
assert_partly_in(gold2, resp, 'datasetAlleleResponses')
def test_deletion_2():
"""Test variantTypes DEL with startMin/startMax."""
query = dict(QUERY)
del query['start']
del query['end']
query['startMin'] = 17301520
query['startMax'] = 17301530
query['endMin'] = 17301535
query['endMax'] = 17301536
query['referenceBases'] = 'ATACATAGTC'
del query['alternateBases']
query['variantType'] = 'DEL'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 2932,
"sampleCount": 2504,
"exists": True,
"referenceBases": "ATACATAGTC",
"alternateBases": "A",
"variantType": "DEL",
"frequency": 0.585463
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_bad_end():
"""Test querying with a bad end position."""
query = dict(QUERY)
query['start'] = 17300407
query['end'] = 17300409
query['referenceBases'] = 'A'
query['alternateBases'] = 'G'
resp = call_beacon(query=query)
assert 'exists' in resp and not resp['exists'], 'Beacon did not report "exist: False" for a bad query'
def test_info():
"""Test the beacon's info (/) call."""
resp = call_beacon(path='/') # takes care of calling, validating to schemas, status code
counts = {"id": "GRCh38:beacon_test:2030-01-01",
"assemblyId": "GRCh38",
"variantCount": 17,
"callCount": 12,
"sampleCount": 2504
}
assert_partly_in(counts, resp, 'datasets')
def run_test(test):
"""Call the beacon as specified in the test and check the result."""
logging.info(f"Running test {test['name']}")
logging.debug(f"{test.get('descr', '')}")
logging.debug(
f"Assuming that this data is present in your beacon: {test.get('data', [])}"
)
settings = utils.setup.Settings()
if test.get('skip', False):
return
try:
status_code, ignore_schemas = prepare_call(test)
if 'query' not in test:
resp = call_beacon(path='/',
code=status_code,
ignore_schemas=ignore_schemas)
else:
query = prepare_query(test['query'])
resp = call_beacon(query=query,
code=status_code,
ignore_schemas=ignore_schemas)
if settings.check_result:
for check in test['results']:
assert_test(check, resp)
except err.ResponseError as r_error:
# errors from the comparisons of a response, contains a list of errors to report
logging.error('Test "%s" did not pass: """%s"""', test['name'],
test['descr'])
for err_msg in r_error.messages:
settings.errors += 1
logging.error(err_msg)
except AssertionError as a_error:
# other errors
logging.error('Test "%s" did not pass: """%s"""', test['name'],
test['descr'])
logging.error(str(a_error))
settings.errors += 1
def test_multi():
"""Test alternateBases=N and multiple variations from one vcf line (indel)."""
query = dict(QUERY)
query['start'] = 19617926
query['referenceBases'] = 'N'
query['alternateBases'] = 'N'
del query['end']
resp = call_beacon(query=query)
golds = [
{"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 17,
"sampleCount": 2504,
"exists": True,
"referenceBases": "GTCT",
"alternateBases": "GTCTTCTTCT",
"variantType": "INS",
"frequency": 0.00339457
},
{"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 118,
"sampleCount": 2504,
"exists": True,
"referenceBases": "GTCT",
"alternateBases": "GTCTTCT",
"variantType": "INS",
"frequency": 0.0235623
},
{"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"variantCount": 182,
"callCount": 5008,
"sampleCount": 2504,
"exists": True,
"referenceBases": "GTCT",
"alternateBases": "G",
"variantType": "DEL",
"frequency": 0.036341853
}]
for gold in golds:
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_end():
"""Test the same query as `test_bad_end()` but with the correct end position."""
query = dict(QUERY)
query['start'] = 17300407
query['end'] = 17300408
query['referenceBases'] = 'A'
query['alternateBases'] = 'G'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 4723,
"sampleCount": 2504,
"exists": True,
"referenceBases": "A",
"alternateBases": "G",
"variantType": "SNP",
"frequency": 0.943091
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_search_1():
"""Test a standard query with alternateBases, start and end."""
query = dict(QUERY)
query['start'] = 16050074
query['end'] = 16050075
query['referenceBases'] = 'A'
query['alternateBases'] = 'G'
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 1,
"sampleCount": 2504,
"exists": True,
"referenceBases": "A",
"alternateBases": "G",
"variantType": "SNP",
"frequency": 0.000199681
}
resp = call_beacon(query=query)
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_deletion_altbase():
"""Test a deletion by searching for ref and alt."""
query = dict(QUERY)
query['start'] = 16497140
query['end'] = 16497143
query['referenceBases'] = 'CTT'
query['alternateBases'] = 'C'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 4,
"sampleCount": 2504,
"exists": True,
"referenceBases": "CTT",
"alternateBases": "C",
"variantType": "DEL",
"frequency": 0.000798722
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_insertion_altbase():
"""Test variantTypes by searching for ref and alt."""
query = dict(QUERY)
query['start'] = 16539540
query['end'] = 16539541
query['referenceBases'] = 'A'
query['alternateBases'] = 'AC'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 7,
"sampleCount": 2504,
"exists": True,
"referenceBases": "A",
"alternateBases": "AC",
"variantType": "INS",
"frequency": 0.00139776
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_snp():
"""Test variantType SNP."""
query = dict(QUERY)
query['start'] = 17302971
query['end'] = 17302972
query['variantType'] = 'SNP'
query['referenceBases'] = 'C'
del query['alternateBases']
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 2931,
"sampleCount": 2504,
"exists": True,
"referenceBases": "C",
"alternateBases": "A",
"variantType": "SNP",
"frequency": 0.585264
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_deletion():
"""Test variantTypes DEL."""
query = dict(QUERY)
query['start'] = 16517679
query['end'] = 16517684
query['referenceBases'] = 'GACAA'
del query['alternateBases']
query['variantType'] = 'DEL'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 3,
"sampleCount": 2504,
"exists": True,
"referenceBases": "GACAA",
"alternateBases": "G",
"variantType": "DEL",
"frequency": 0.000599042
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_snp_mnp():
"""Test representation of TG->AG and multiple variations from one vcf line."""
query = dict(QUERY)
query['start'] = 16577043
query['end'] = 16577045
query['referenceBases'] = 'TG'
del query['alternateBases']
query['variantType'] = 'SNP'
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 17,
"sampleCount": 2504,
"exists": True,
"referenceBases": "TG",
"alternateBases": "AG",
"variantType": "SNP",
"frequency": 0.003394569
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')
def test_insertion():
"""Test variantTypes INS."""
query = dict(QUERY)
query['start'] = 16064512
query['end'] = 16064513
query['variantType'] = 'INS'
query['referenceBases'] = 'A'
del query['alternateBases']
resp = call_beacon(query=query)
gold = {"datasetId": "GRCh38:beacon_test:2030-01-01",
"referenceName": "22",
"callCount": 5008,
"variantCount": 21,
"sampleCount": 2504,
"exists": True,
"referenceBases": "A",
"alternateBases": "AAGAATGGCCTAATAC",
"variantType": "INS",
"frequency": 0.00419329
}
assert_partly_in(gold, resp, 'datasetAlleleResponses')