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) 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) 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) 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 test_base_case_no_coverage(self): pc = ProbeCoverage(min_depth=0, percent_coverage=0, median_depth=0) s1 = SequenceProbeCoverage(name="A123T", probe_coverage=pc ) call = self.pt.type(s1) assert call.genotype == [0, 0]
def test_resistotype_gene_at_high_CN(self): pc = ProbeCoverage(min_depth=100, percent_coverage=100, median_depth=1000) 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) s = SequenceProbeCoverage(name="A123T", probe_coverage=pc, percent_coverage_threshold=80 ) call = self.pt.type(s) assert call.genotype == [0, 1]
def _parse_seq_panel(self, row): allele, median_depth, min_depth, percent_coverage, k_count = self._parse_summary_covgs_row( row) probe_coverage = ProbeCoverage(percent_coverage=percent_coverage, median_depth=median_depth, min_depth=min_depth, k_count=k_count) allele_name = allele.split('?')[0] params = get_params(allele) panel_type = params.get("panel_type", "presence") name = params.get('name') version = params.get('version', '1') if panel_type in ["variant", "presence"]: sequence_probe_coverage = SequenceProbeCoverage( name=name, probe_coverage=probe_coverage, version=version, length=params.get("length")) try: self.covgs[panel_type][name][version] = sequence_probe_coverage except KeyError: self.covgs[panel_type][name] = {} self.covgs[panel_type][name][version] = sequence_probe_coverage else: # Species panels are treated differently l = int(params.get("length", -1)) try: self.covgs[panel_type][name]["total_bases"] += l if percent_coverage > 75 and median_depth > 0: self.covgs[panel_type][name]["percent_coverage"].append( percent_coverage) self.covgs[panel_type][name]["length"].append(l) self.covgs[panel_type][name]["median"].append(median_depth) except KeyError: if panel_type not in self.covgs: self.covgs[panel_type] = {} self.covgs[panel_type][name] = {} self.covgs[panel_type][name]["total_bases"] = l if percent_coverage > 75 and median_depth > 0: self.covgs[panel_type][name]["percent_coverage"] = [ percent_coverage ] self.covgs[panel_type][name]["length"] = [l] self.covgs[panel_type][name]["median"] = [median_depth] else: self.covgs[panel_type][name]["percent_coverage"] = [] self.covgs[panel_type][name]["length"] = [] self.covgs[panel_type][name]["median"] = []
def test_low_coverage(self): pc = ProbeCoverage(min_depth=100, percent_coverage=16, median_depth=16) 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) s = SequenceProbeCoverage(name="A123T", probe_coverage=pc, percent_coverage_threshold=80 ) call = self.pt_10.type(s) assert call.genotype == [1, 1]