def setUp(self):
self.variant_snp = Variant.create(start=0,
end=1,
reference_bases="A",
alternate_bases=["T"])
self.predictor = TBPredictor(variant_calls={}, called_genes={})
def setUp(self):
self.variant_snp = Variant.create(start=0,
end=1,
reference_bases="A",
alternate_bases=["T"])
self.predictor = TBPredictor(
variant_calls={},
called_genes={},
variant_to_resistance_json_fp=os.path.join(
DATA_DIR, "tb_variant_to_resistance_drug.json"))
class AMRPredictTest(TestCase):
def setUp(self):
self.variant_snp = Variant.create(
start=0, end=1, reference_bases="A", alternate_bases=["T"]
)
self.predictor = TBPredictor(variant_calls={}, called_genes={})
def teardown(self):
pass
def test_wt_vars(self):
call = {
"variant": None,
"genotype": [0, 1],
"genotype_likelihoods": [0.1, 0.9, 0.12],
"info": {
"contamination_depths": [],
"coverage": {
"alternate": {
"percent_coverage": 100.0,
"median_depth": 15,
"min_depth": 2,
},
"reference": {
"percent_coverage": 100.0,
"median_depth": 139,
"min_depth": 128,
},
},
"expected_depths": [152],
},
}
assert self.predictor._coverage_greater_than_threshold(call, [""]) is False
class AMRPredictTest(TestCase):
def setUp(self):
self.variant_snp = Variant.create(start=0, end=1, reference_bases="A",
alternate_bases=["T"])
self.predictor = TBPredictor(variant_calls={},
called_genes={})
def teardown(self):
pass
def test_wt_vars(self):
call = {
"variant": None,
"genotype": [
0,
1],
"genotype_likelihoods": [
0.1,
0.9,
0.12],
"info": {
"contamination_depths": [],
"coverage": {
"alternate": {
"percent_coverage": 100.0,
"median_depth": 15,
"min_depth": 2},
"reference": {
"percent_coverage": 100.0,
"median_depth": 139,
"min_depth": 128}},
"expected_depths": [152]}}
assert self.predictor._coverage_greater_than_threshold(call, [
""]) == False
def setUp(self):
self.variant_snp = Variant.create(start=0, end=1, reference_bases="A",
alternate_bases=["T"])
self.predictor = TBPredictor(variant_calls={},
called_genes={})