def test_alleleHasNoSeparator_raisesError(self):
row = ",".join(
["lineage1", "615938", "1104", "GA", "368", "GAG/GAA", "E/E", "foo", "",]
)
with pytest.raises(ValueError):
PanelVariant.from_row(row)
def test_geneNameIsEmpty_returnsNone(self):
row = ",".join(
["lineage1", "615938", "1104", "G/A", "368", "GAG/GAA", "E/E", "foo", "",]
)
actual = PanelVariant.from_row(row)
expected = PanelVariant(Lineage("1"), 615938, "G", "A", "foo", None, 1104)
assert actual == expected
def test_tabAsDelim_returnsExpected(self):
delim = "\t"
row = delim.join(
["lineage1", "615938", "1104", "G/A", "368", "GAG/GAA", "E/E", "foo", "",]
)
actual = PanelVariant.from_row(row, delim=delim)
expected = PanelVariant(Lineage("1"), 615938, "G", "A", "foo", None, 1104)
assert actual == expected
def test_noHeader_allPanelVariantsInPanel(self):
stream = StringIO(
"lineage1,615938,1104,G/A,368,GAG/GAA,E/E,Rv0524,hemL\n"
"lineage1.1,4404247,1056,G/A,352,CTG/CTA,L/L,Rv3915,-"
)
actual = load_panel(stream)
expected = {
615938: PanelVariant(
Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", 1104
),
4404247: PanelVariant(
Lineage("1", "1"), 4404247, "G", "A", "Rv3915", "-", 1056
),
}
assert actual == expected
def test_fileWithNoIssues_loadsOk(self):
stream = StringIO(
"lineage,position,gene_coord,allele_change,codon_number,codon_change,amino_acid_change,locus_id,gene_name\n"
"lineage1,615938,1104,G/A,368,GAG/GAA,E/E,Rv0524,hemL\n"
"lineage1.1,4404247,1056,G/A,352,CTG/CTA,L/L,Rv3915,-"
)
actual = load_panel(stream, no_header=False)
expected = {
615938: PanelVariant(
Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", 1104
),
4404247: PanelVariant(
Lineage("1", "1"), 4404247, "G", "A", "Rv3915", "-", 1056
),
}
assert actual == expected
def test_nonDefaultDelim_loadsOk(self):
stream = StringIO(
"lineage1|615938|1104|G/A|368|GAG/GAA|E/E|Rv0524|hemL\n"
"lineage1.1|4404247|1056|G/A|352|CTG/CTA|L/L|Rv3915|-"
)
delim = "|"
actual = load_panel(stream, delim=delim)
expected = {
615938: PanelVariant(
Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", 1104
),
4404247: PanelVariant(
Lineage("1", "1"), 4404247, "G", "A", "Rv3915", "-", 1056
),
}
assert actual == expected
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_geneCoordIsntInt_returnsNone(self):
row = ",".join(
[
"lineage1",
"615938",
"foo",
"G/A",
"368",
"GAG/GAA",
"E/E",
"Rv0524",
"hemL",
]
)
actual = PanelVariant.from_row(row)
expected = PanelVariant(Lineage("1"), 615938, "G", "A", "Rv0524", "hemL", None)
assert actual == expected
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_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_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_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
def test_rowPositionFieldMissing_raisesError(self):
row = "foo,,,,"
with pytest.raises(ValueError):
PanelVariant.from_row(row)
def test_rowWithNoFields_raisesError(self):
row = ",,,,"
with pytest.raises(RowError):
PanelVariant.from_row(row)
def test_emptyRow_raisesError(self):
row = ""
with pytest.raises(RowError):
PanelVariant.from_row(row)
