def test_genotyping_gene_11(self):
pt_no_contaim = PresenceTyper(expected_depths=[20])
pt_contaim = PresenceTyper(
expected_depths=[20],
contamination_depths=[10])
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=10,
k_count=100,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = pt_no_contaim.type(s)
assert call.genotype == [1, 1]
call = pt_contaim.type(s)
assert call.genotype == [0, 0]
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=30,
k_count=30,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = pt_no_contaim.type(s)
assert call.genotype == [1, 1]
call = pt_contaim.type(s)
assert call.genotype == [1, 1]
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=20,
k_count=20,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = pt_no_contaim.type(s)
assert call.genotype == [1, 1]
call = pt_contaim.type(s)
assert call.genotype == [1, 1]
def setUp(self):
self.pt = PresenceTyper(expected_depths=[100])
self.pt_10 = PresenceTyper(expected_depths=[10])
class PresenceTyperTest(TestCase):
def setUp(self):
self.pt = PresenceTyper(expected_depths=[100])
self.pt_10 = PresenceTyper(expected_depths=[10])
def teardown(self):
pass
def test_base_case_no_coverage(self):
pc = ProbeCoverage(min_depth=0,
percent_coverage=0,
median_depth=0,
k_count=0,
klen=31)
s1 = SequenceProbeCoverage(name="A123T",
probe_coverage=pc
)
call = self.pt.type(s1)
assert call.genotype == [0, 0]
def test_genotyping_gene_11(self):
pc = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=100,
k_count=100,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = self.pt.type(s)
assert call.genotype == [1, 1]
def test_genotyping_gene_01(self):
pc = ProbeCoverage(min_depth=100,
percent_coverage=82,
median_depth=2,
k_count=82,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = self.pt.type(s)
assert call.genotype == [0, 1]
def test_resistotype_gene_at_high_CN(self):
pc = ProbeCoverage(min_depth=100,
percent_coverage=100,
median_depth=1000,
k_count=100,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = self.pt.type(s)
assert call.genotype == [1, 1]
def test_low_coverage(self):
pc = ProbeCoverage(min_depth=100,
percent_coverage=16,
median_depth=16,
k_count=16,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = self.pt_10.type(s)
assert call.genotype == [0, 0]
pc = ProbeCoverage(min_depth=100,
percent_coverage=80,
median_depth=16,
k_count=16,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = self.pt_10.type(s)
assert call.genotype == [1, 1]
def setUp(self):
self.pt_no_contaim = PresenceTyper(expected_depths=[100])
self.pt_contaim = PresenceTyper(
expected_depths=[100],
contamination_depths=[10])
class PresenceTyperTestWithContaim(TestCase):
def setUp(self):
self.pt_no_contaim = PresenceTyper(expected_depths=[100])
self.pt_contaim = PresenceTyper(
expected_depths=[100],
contamination_depths=[10])
def teardown(self):
pass
def test_genotyping_gene_01(self):
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=10,
k_count=10,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = self.pt_no_contaim.type(s)
assert call.genotype == [0, 1]
call = self.pt_contaim.type(s)
assert call.genotype == [0, 0]
def test_genotyping_gene_11(self):
pt_no_contaim = PresenceTyper(expected_depths=[20])
pt_contaim = PresenceTyper(
expected_depths=[20],
contamination_depths=[10])
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=10,
k_count=100,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = pt_no_contaim.type(s)
assert call.genotype == [1, 1]
call = pt_contaim.type(s)
assert call.genotype == [0, 0]
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=30,
k_count=30,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = pt_no_contaim.type(s)
assert call.genotype == [1, 1]
call = pt_contaim.type(s)
assert call.genotype == [1, 1]
pc = ProbeCoverage(min_depth=10,
percent_coverage=100,
median_depth=20,
k_count=20,
klen=31)
s = SequenceProbeCoverage(name="A123T",
probe_coverage=pc,
percent_coverage_threshold=80
)
call = pt_no_contaim.type(s)
assert call.genotype == [1, 1]
call = pt_contaim.type(s)
assert call.genotype == [1, 1]