def test_write(self):
qfile = io.QFile()
qfile.add("A", [1, 1, 1])
qfile.add("B", [1, 1, 1])
qfile.add("C", [1, 1, 1])
stream = StringIO("")
qfile.write(stream)
expected = "A\t1\t1\t1\nB\t1\t1\t1\nC\t1\t1\t1\n"
assert stream.getvalue() == expected
def test_barplot(self):
qfile = io.QFile()
qfile.add("A", [1, 1, 1])
qfile.add("B", [2, 2, 2])
qfile.add("C", [3, 3, 3])
barplot = qfile.to_barplot()
expected = [
dict(x=["A", "B", "C"], y=[1, 2, 3], type="bar", name="Pop #000"),
dict(x=["A", "B", "C"], y=[1, 2, 3], type="bar", name="Pop #001"),
dict(x=["A", "B", "C"], y=[1, 2, 3], type="bar", name="Pop #002")
]
for i in range(3):
assert barplot[i] == expected[i]
def test_summarise(self):
qfile = io.QFile()
qfile.add("A", [1, 1, 1])
qfile.add("B", [1, 1, 1])
qfile.add("C", [1, 1, 1])
qfile.add("D", [1, 1, 1])
qfile.add("E", [1, 1, 1])
qfile.add("F", [1, 1, 1])
qfile = qfile.summarise(["GA", "GB"], [(1, 3), (4, 6)])
assert qfile.samples == ["A", "D", "GA", "GB"]
assert qfile.get_ancestry(0) == [1, 1, 1, 1]
assert qfile.get_ancestry(1) == [1, 1, 1, 1]
assert qfile.get_ancestry(2) == [1, 1, 1, 1]
def test_iterate_ancestry(self):
qfile = io.QFile()
qfile.add("X", [0, 1, 2])
for sample, ancestry in qfile:
assert sample == "X"
assert ancestry == [0, 1, 2]
def test_add(self):
qfile = io.QFile()
qfile.add("X", [0, 1, 2])
assert qfile.n_ancestries == 3
assert qfile.n_samples == 1
def test_get_ancestry_raise_error(self):
qfile = io.QFile()
with pytest.raises(IndexError):
qfile.get_ancestry(1)
def test_create_empty(self):
qfile = io.QFile()
assert qfile.n_samples == 0
assert qfile.n_ancestries == 0