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]