def test_is_valid(self):
"""Enumeration is_valid should return True for valid sequence"""
a = Enumeration("bca")
self.assertEqual(a.is_valid(""), True)
self.assertEqual(a.is_valid("bbb"), True)
self.assertEqual(a.is_valid("bbbaac"), True)
self.assertEqual(a.is_valid("bbd"), False)
self.assertEqual(a.is_valid("d"), False)
self.assertEqual(a.is_valid(["a", "b"]), True)
self.assertEqual(a.is_valid(["a", None]), False)
def test_mul(self):
"""Enumeration mul should produce correct JointEnumeration"""
a = DnaBases * RnaBases
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("G", "G"))
# check that it works with gaps
a = Enumeration("ab-", "-")
b = Enumeration("xz", "z")
x = a * b
self.assertEqual(x.gap, ("-", "z"))
self.assertEqual(x.gap_index, 5)
self.assertEqual(len(x), 6)
self.assertEqual(x, (("a", "x"), ("a", "z"), ("b", "x"), ("b", "z"),
("-", "x"), ("-", "z")))
# check that it doesn't work when only one seq has gaps
c = Enumeration("c")
x = a * c
self.assertEqual(x.gap, None)
def test_pow(self):
"""Enumeration pow should produce JointEnumeration with n copies"""
a = AminoAcids**3
self.assertEqual(a[0], (AminoAcids[0], ) * 3)
self.assertEqual(a[-1], (AminoAcids[-1], ) * 3)
self.assertEqual(len(a), len(AminoAcids)**3)
self.assertEqual(a.array_type, uint16)
# check that it works with gaps
a = Enumeration("a-b", "-")
b = a**3
self.assertEqual(len(b), 27)
self.assertEqual(b.gap, ("-", "-", "-"))
self.assertEqual(b.gap_index, 13)
self.assertEqual(b.array_type, uint8)
# check that array type is set correctly if needed
b = a**6 # too big to fit in char
self.assertEqual(b.array_type, uint16)
def test_init(self):
"""Enumeration init should work from any sequence"""
a = Enumeration("abc")
self.assertEqual(a.index("a"), 0)
self.assertEqual(a.index("b"), 1)
self.assertEqual(a.index("c"), 2)
self.assertEqual(a[0], "a")
self.assertEqual(a[1], "b")
self.assertEqual(a[2], "c")
self.assertEqual(a.array_type, uint8)
a = Enumeration("bca")
self.assertEqual(a.index("b"), 0)
self.assertEqual(a.index("c"), 1)
self.assertEqual(a.index("a"), 2)
self.assertEqual(a[0], "b")
self.assertEqual(a[1], "c")
self.assertEqual(a[2], "a")
a = Enumeration([1, "2"])
self.assertEqual(a.index(1), 0)
self.assertEqual(a.index("2"), 1)
self.assertRaises(KeyError, a.index, "1")
# check that it works with gaps
a = Enumeration("ab-", "-")
self.assertEqual(a.gap, "-")
self.assertEqual(a.gap_index, 2)
a = Enumeration(list(range(257))) # too big to fit in uint8
self.assertEqual(a.array_type, uint16)
def test_from_indices(self):
"""Enumeration from_indices should return elements from indices"""
a = Enumeration("bca")
self.assertEqual(a.from_indices([]), [])
self.assertEqual(a.from_indices([1, 1, 2, 0, 2, 1]), list("ccabac"))
def test_to_indices(self):
"""Enumeration to_indices should return indices from elements"""
a = Enumeration("bca")
self.assertEqual(a.to_indices(""), [])
self.assertEqual(a.to_indices("ccabac"), [1, 1, 2, 0, 2, 1])
def test_getitem(self):
"""Enumeration[i] should return character at i"""
a = Enumeration("bca")
self.assertEqual(a[0], "b")
self.assertEqual(a[1], "c")
self.assertEqual(a[2], "a")
def test_index(self):
"""Enumeration index should return first index of item"""
a = Enumeration("bca")
self.assertEqual(a.index("b"), 0)
self.assertEqual(a.index("c"), 1)
self.assertEqual(a.index("a"), 2)