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_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_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)