class VariantTyperWithContamination(TestCase):
def setUp(self):
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[])
# To do add contamination type
# self.vt_contaim = VariantTyper(
# expected_depths=[80],
# contamination_depths=[20])
def teardown(self):
pass
def test_simple_case(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=80,
k_count=80)
alternate_coverages = [
ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=20,
k_count=40)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [0, 1]
class TestVariantTyperWithMultipleAlternateCoverages(TestCase):
def setUp(self):
# to do, test should pass on kc model also
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[],
model="median_depth")
def teardown(self):
pass
def test_simple_case(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=70,
median_depth=80,
k_count=80)
alt1 = ProbeCoverage(min_depth=100,
percent_coverage=70,
median_depth=20,
k_count=20)
alt2 = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=80,
k_count=80)
alternate_coverages = [alt1, alt2]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
assert v1._choose_best_alternate_coverage() == alt2
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [1, 1]
class TestVariantTyperWithMultipleProbeCoverages(TestCase):
def setUp(self):
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[])
def teardown(self):
pass
def test_simple_case(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=80,
median_depth=80,
k_count=80,
klen=31)
alt1 = ProbeCoverage(min_depth=100,
percent_coverage=50,
median_depth=20,
k_count=20,
klen=31)
alt2 = ProbeCoverage(min_depth=100,
percent_coverage=40,
median_depth=80,
k_count=30,
klen=31)
alternate_coverages = [alt1, alt2]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=80,
median_depth=80,
k_count=20,
klen=31)
alt1 = ProbeCoverage(min_depth=100,
percent_coverage=50,
median_depth=20,
k_count=20,
klen=31)
alt2 = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=80,
k_count=100,
klen=31)
alternate_coverages = [alt1, alt2]
v2 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type([v1, v2])
assert call['genotype'] == [1, 1]
def test_4(self):
vt = VariantTyper(expected_depths=[6],
contamination_depths=[],
confidence_threshold=3)
reference_coverage = ProbeCoverage(min_depth=1,
percent_coverage=100,
median_depth=2,
k_count=2)
alt1 = ProbeCoverage(min_depth=1,
percent_coverage=100,
median_depth=1,
k_count=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = vt.type(v1)
assert call['genotype'] == [0, 1]
print(call["info"])
assert call["info"]["conf"] < 100
class VariantTyperTest(TestCase):
def setUp(self):
self.vt = VariantTyper(expected_depths=[100])
def teardown(self):
pass
def test_wt_vars(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=100,
k_count=100)
alternate_coverages = [
ProbeCoverage(min_depth=100,
percent_coverage=3,
median_depth=100,
k_count=3)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt.type([v1])
assert call['genotype'] == [0, 0]
assert call["info"].get('expected_depths') == [100]
def test_alt_vars(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=3,
median_depth=100,
k_count=3)
alternate_coverages = [
ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=100,
k_count=100)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt.type([v1])
assert call['genotype'] == [1, 1]
def test_mixed_vars(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=50,
k_count=50)
alternate_coverages = [
ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=50,
k_count=50)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt.type(v1)
assert call['genotype'] == [0, 1]
def test_mixed_vars2(self):
reference_coverage = ProbeCoverage(min_depth=11,
percent_coverage=100,
median_depth=42,
k_count=42)
alternate_coverages = [
ProbeCoverage(min_depth=94,
percent_coverage=100,
median_depth=102,
k_count=94)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt.type(v1)
assert call['genotype'] == [0, 1]
class TestVariantTyperWithLowMinimum(TestCase):
def setUp(self):
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[])
self.vt2_no_contaim = VariantTyper(expected_depths=[1],
contamination_depths=[])
def teardown(self):
pass
def test_2(self):
reference_coverage = ProbeCoverage(min_depth=131,
percent_coverage=95.2381,
median_depth=155,
k_count=131)
alt1 = ProbeCoverage(min_depth=1,
percent_coverage=100,
median_depth=1,
k_count=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [0, 0]
def test_3(self):
reference_coverage = ProbeCoverage(min_depth=2,
percent_coverage=59.52,
median_depth=2,
k_count=60)
alt1 = ProbeCoverage(min_depth=1,
percent_coverage=83.33,
median_depth=1,
k_count=83)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = self.vt2_no_contaim.type(v1)
assert call['genotype'] == [1, 1]
assert call["info"]["conf"] < 100
def test_4(self):
vt = VariantTyper(expected_depths=[6],
contamination_depths=[],
confidence_threshold=3)
reference_coverage = ProbeCoverage(min_depth=1,
percent_coverage=100,
median_depth=2,
k_count=2)
alt1 = ProbeCoverage(min_depth=1,
percent_coverage=100,
median_depth=1,
k_count=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverages=[reference_coverage],
alternate_coverages=alternate_coverages)
call = vt.type(v1)
assert call['genotype'] == [0, 1]
print(call["info"])
assert call["info"]["conf"] < 100