def test_variantRefDoesntMatchPanel_returnsFalse(self, mock_variant):
index = {
1: PanelVariant(Lineage("1"), 1, "G", "A"),
}
classifier = Classifier(index)
mock_variant.POS = 1
mock_variant.REF = "d"
mock_variant.FILTER = None
assert not classifier.is_variant_valid(mock_variant)
def test_posNotInPanel_returnsFalse(self, mock_variant):
index = {
1: PanelVariant(Lineage("1"), 1, "G", "A"),
}
classifier = Classifier(index)
mock_variant.POS = 4
mock_variant.REF = "G"
mock_variant.FILTER = None
assert not classifier.is_variant_valid(mock_variant)
def test_panelVariantFailsFilter_returnsFalse(self, mock_variant):
index = {
1: PanelVariant(Lineage("1"), 1, "G", "A"),
}
classifier = Classifier(index)
mock_variant.POS = 1
mock_variant.REF = "G"
mock_variant.ALT = ["T", "A"]
mock_variant.FILTER = "FAIL"
assert not classifier.is_variant_valid(mock_variant)
def test_refLineagePosPanelRefInAlt_returnsTrue(self, mock_variant):
index = {
1: PanelVariant(Lineage("1"), 1, "G", "A"),
}
classifier = Classifier(index)
mock_variant.POS = 1
mock_variant.REF = "G"
mock_variant.ALT = ["T", "C"]
mock_variant.FILTER = None
assert not classifier.is_variant_valid(mock_variant)
def test_panelVariantAltNotInVariantAlts_returnsFalse(self, mock_variant):
index = {
1: PanelVariant(Lineage("1"), 1, "G", "A"),
}
classifier = Classifier(index)
mock_variant.POS = 1
mock_variant.REF = "G"
mock_variant.ALT = ["T", "C"]
mock_variant.FILTER = None
assert not classifier.is_variant_valid(mock_variant)
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)
