def test_oneLineage_returnsOnlyElement(self):
l1 = Lineage(major="4", minor="1.3.4")
classifier = Classifier()
sample_idx = 0
actual = classifier.call_sample_lineage([l1], sample_idx)
expected = str(l1)
assert actual == expected
def test_emptyList_returnsNone(self):
lineages = []
classifier = Classifier()
sample_idx = 0
expected = "unknown"
actual = classifier.call_sample_lineage(lineages, sample_idx, default=expected)
assert actual == expected
def test_twoLineagesDiffMajor_returnsMixedDisregardMaxAlt(self):
l1 = Lineage(major="4", minor="1.3.4")
l2 = Lineage(major="5", minor="8.3")
classifier = Classifier(max_alt_lineages=5)
sample_idx = 0
actual = classifier.call_sample_lineage([l1, l2], sample_idx)
expected = "mixed"
assert actual == expected
def test_twoLineagesSameMajor_returnsLowestOnTree(self):
l1 = Lineage(major="4", minor="1.3.4")
l2 = Lineage(major="4", minor="8.3")
classifier = Classifier()
sample_idx = 0
actual = classifier.call_sample_lineage([l1, l2], sample_idx)
expected = str(l1)
assert actual == expected
def test_oneLineageTooManyHets_returnsTooManyHets(self):
l1 = Lineage(major="4", minor="1.3.4")
classifier = Classifier(max_het=1)
sample_idx = 0
classifier.het_counts[sample_idx] = 5
actual = classifier.call_sample_lineage([l1], sample_idx)
expected = "too_many_hets"
assert actual == expected
def test_mixedLineagesBelowThreshold_returnsMostCommon(self):
l1 = Lineage(major="4", minor="1.3.4")
l2 = Lineage(major="4", minor="1.3")
l3 = Lineage(major="5", minor="8.3")
classifier = Classifier(max_alt_lineages=1)
sample_idx = 0
actual = classifier.call_sample_lineage([l1, l2, l3], sample_idx)
expected = str(l1)
assert actual == expected
