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 _parse_variant_panel(self, row): allele, median_depth, min_depth, percent_coverage, k_count = self._parse_summary_covgs_row( row) params = get_params(allele) if 'var_name' in params: var_name = params.get('var_name') else: var_name = allele.split('?')[0].split('-')[1] num_alts = int(params.get("num_alts", 0)) reference_coverages = [ ProbeCoverage(percent_coverage=percent_coverage, median_depth=median_depth, min_depth=min_depth, k_count=k_count) ] alt_or_ref = 'ref' alternate_coverages = [] for i in range(num_alts - 1): row = next(self.reader) ref_allele, median_depth, min_depth, percent_coverage, k_count = self._parse_summary_covgs_row( row) if ref_allele.split('-')[0] != 'ref': logger.warning("Fewer ref alleles than alt alleles for %s" % ref_allele) alternate_coverages.append( ProbeCoverage(min_depth=min_depth, k_count=k_count, percent_coverage=percent_coverage, median_depth=median_depth)) num_alts -= 1 break assert ref_allele.split('-')[0] == 'ref' reference_coverages.append( ProbeCoverage(percent_coverage=percent_coverage, median_depth=median_depth, min_depth=min_depth, k_count=k_count)) for i in range(num_alts): row = next(self.reader) alt_allele, median_depth, min_depth, percent_coverage, k_count = self._parse_summary_covgs_row( row) assert alt_allele.split('-')[0] == 'alt' alternate_coverages.append( ProbeCoverage(min_depth=min_depth, k_count=k_count, percent_coverage=percent_coverage, median_depth=median_depth)) variant_probe_coverage = VariantProbeCoverage( reference_coverages=reference_coverages, alternate_coverages=alternate_coverages, var_name=var_name, params=params) try: self.variant_covgs[allele].append(variant_probe_coverage) except KeyError: self.variant_covgs[allele] = [variant_probe_coverage]
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]
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]
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_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_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]
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_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 _parse_variant_panel(self, row): ( probe, median_depth, min_depth, percent_coverage, k_count, klen, ) = self._parse_summary_covgs_row(row) params = get_params(probe) probe_type = probe.split("-")[0] if "var_name" in params: var_name = (params.get("gene", "") + "_" + params.get("mut", "") + "-" + params.get("var_name", "")) else: var_name = allele.split("?")[0].split("-")[1] if not var_name in self.variant_covgs: variant_probe_coverage = VariantProbeCoverage( reference_coverages=[], alternate_coverages=[], var_name=probe, params=params, ) self.variant_covgs[var_name] = variant_probe_coverage probe_coverage = ProbeCoverage( min_depth=min_depth, k_count=k_count, percent_coverage=percent_coverage, median_depth=median_depth, klen=klen, ) if probe_type == "ref": self.variant_covgs[var_name].reference_coverages.append( probe_coverage) self.variant_covgs[ var_name].best_reference_coverage = self.variant_covgs[ var_name]._choose_best_reference_coverage() elif probe_type == "alt": self.variant_covgs[var_name].alternate_coverages.append( probe_coverage) self.variant_covgs[ var_name].best_alternate_coverage = self.variant_covgs[ var_name]._choose_best_alternate_coverage() else: raise ValueError("probe_type must be ref or alt")
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