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]