def test_sampleHasLineageVariantAndPassesFilter_returnsIndex(self, mocked_variant): index = { 1: PanelVariant(Lineage("1"), 1, "G", "A"), } classifier = Classifier(index) mocked_variant.POS = 1 mocked_variant.REF = "G" mocked_variant.ALT = ["T", "A", "N"] mocked_variant.genotypes = [[-1, -1, False], [2, 2, False]] mocked_variant.format.return_value = ["PASS", "PASS"] actual = classifier.samples_with_lineage_variant(mocked_variant) expected = [1] assert actual == expected
def test_hetSampleDoesntHaveLineageVariant_returnsEmpty(self, mocked_variant): index = { 1: PanelVariant(Lineage("1"), 1, "G", "A"), } classifier = Classifier(index) mocked_variant.POS = 1 mocked_variant.REF = "G" mocked_variant.ALT = ["T", "A", "N"] mocked_variant.genotypes = [[-1, -1, False], [1, 3, False]] mocked_variant.format.side_effect = KeyError actual = classifier.samples_with_lineage_variant(mocked_variant) expected = [] assert actual == expected
def test_posNotInPanel_returnsEmpty(self, mocked_variant): index = { 4: PanelVariant(Lineage("1"), 1, "G", "A"), } classifier = Classifier(index) mocked_variant.POS = 1 mocked_variant.REF = "G" mocked_variant.ALT = ["T", "A"] mocked_variant.genotypes = [[2, -1, False], [2, 2, False]] mocked_variant.format.side_effect = KeyError actual = classifier.samples_with_lineage_variant(mocked_variant) expected = [] assert actual == expected
def test_allSamplesHaveLineageVariant_returnsAllIndices(self, mocked_variant): index = { 1: PanelVariant(Lineage("1"), 1, "G", "A"), } classifier = Classifier(index) mocked_variant.POS = 1 mocked_variant.REF = "G" mocked_variant.ALT = ["T", "A"] mocked_variant.genotypes = [[2, -1, False], [2, 2, False]] mocked_variant.format.side_effect = KeyError actual = classifier.samples_with_lineage_variant(mocked_variant) expected = [0, 1] assert actual == expected
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_hetSampleHasLineageVariantIncludeHetAndIncrementHetCount_returnsHetIndex( self, mocked_variant ): index = { 1: PanelVariant(Lineage("1"), 1, "G", "A"), } classifier = Classifier(index) mocked_variant.POS = 1 mocked_variant.REF = "G" mocked_variant.ALT = ["T", "A"] mocked_variant.genotypes = [[-1, -1, False], [2, 0, False]] mocked_variant.format.side_effect = KeyError actual = classifier.samples_with_lineage_variant(mocked_variant) expected = [1] assert actual == expected assert classifier.het_counts[1] == 1