def test_majorAndMinor_allMinorsLumpedInTogether(self):
s = "lineage4.1.2.3.4.5"
actual = Lineage.from_str(s)
expected = Lineage(major="4", minor="1.2.3.4.5")
assert actual == expected
def test_onlyMajor_minorIsNone(self):
s = "lineage4"
actual = Lineage.from_str(s).minor
expected = ()
assert actual == expected
def test_withPrefixLineage_ignoresPrefix(self):
s = "lineageBovis"
actual = Lineage.from_str(s)
expected = Lineage(major="Bovis")
assert actual == expected
def test_panelVariantAltIsNotVariantRef_returnsFalse(self, mock_variant):
pos = 1692141
index = {
pos: PanelVariant(Lineage.from_str("4.10"), position=pos, ref="C", alt="T"),
}
classifier = Classifier(index, ref_lineage_position=pos)
mock_variant.POS = pos
mock_variant.REF = "A"
mock_variant.ALT = ["C"]
mock_variant.FILTER = None
assert not classifier.is_variant_valid(mock_variant)
def test_panelVariantAltIsVariantRefForRefLineagePos_returnsIndex(
self, mock_variant
):
pos = 1692141
index = {
pos: PanelVariant(Lineage.from_str("4.10"), position=pos, ref="C", alt="A"),
}
classifier = Classifier(index, ref_lineage_position=pos)
mock_variant.POS = pos
mock_variant.REF = "A"
mock_variant.ALT = ["C"]
mock_variant.genotypes = [[0, 0, False], [1, 1, False]]
mock_variant.format.return_value = ["PASS", "PASS"]
actual = classifier.samples_with_lineage_variant(mock_variant)
expected = [0]
assert actual == expected
def test_emptyString_raisesError(self):
s = ""
with pytest.raises(InvalidLineageString):
Lineage.from_str(s)