class VariantTyperWithContamination(TestCase):
def setUp(self):
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[])
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)
alternate_coverages = [
ProbeCoverage(min_depth=100, percent_coverage=100, median_depth=20)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [0, 1]
call = self.vt_contaim.type(v1)
assert call['genotype'] == [0, 0]
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)
alt1 = ProbeCoverage(min_depth=1, percent_coverage=100, median_depth=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = vt.type(v1)
assert call['genotype'] == [0, 1]
assert call["info"]["filter"] == "LOW_GT_CONF"
class TestVariantTyperWithMultipleAlternateCoverages(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=70,
median_depth=80)
alt1 = ProbeCoverage(min_depth=100,
percent_coverage=70,
median_depth=20)
alt2 = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=80)
alternate_coverages = [alt1, alt2]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=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 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)
alternate_coverages = [
ProbeCoverage(min_depth=100, percent_coverage=3, median_depth=100)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=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)
alternate_coverages = [
ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=100)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=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)
alternate_coverages = [
ProbeCoverage(min_depth=100, percent_coverage=100, median_depth=50)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=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)
alternate_coverages = [
ProbeCoverage(min_depth=94, percent_coverage=100, median_depth=102)
]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = self.vt.type(v1)
assert call['genotype'] == [0, 1]
def setUp(self):
self.vt_no_contaim = VariantTyper(expected_depths=[100],
contamination_depths=[])
self.vt_contaim = VariantTyper(expected_depths=[80],
contamination_depths=[20])
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_simple_case(self):
reference_coverage = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=100)
alt1 = ProbeCoverage(min_depth=80,
percent_coverage=100,
median_depth=100)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [0, 1]
alt1 = ProbeCoverage(min_depth=1,
percent_coverage=100,
median_depth=100)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [0, 0]
def test_2(self):
reference_coverage = ProbeCoverage(min_depth=131,
percent_coverage=95.2381,
median_depth=155)
alt1 = ProbeCoverage(min_depth=1, percent_coverage=100, median_depth=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = self.vt_no_contaim.type(v1)
assert call['genotype'] == [0, 0]
assert call["info"]["filter"] != "PASS"
def test_3(self):
reference_coverage = ProbeCoverage(min_depth=2,
percent_coverage=59.52,
median_depth=2)
alt1 = ProbeCoverage(min_depth=1,
percent_coverage=83.33,
median_depth=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = self.vt2_no_contaim.type(v1)
assert call['genotype'] == [1, 1]
assert call["info"]["filter"] != "PASS"
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)
alt1 = ProbeCoverage(min_depth=1, percent_coverage=100, median_depth=1)
alternate_coverages = [alt1]
v1 = VariantProbeCoverage(var_name="A123T",
reference_coverage=reference_coverage,
alternate_coverages=alternate_coverages)
call = vt.type(v1)
assert call['genotype'] == [0, 1]
assert call["info"]["filter"] == "LOW_GT_CONF"
def setUp(self):
self.vt = VariantTyper(expected_depths=[100])