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)