def test_init(self):
"""JointEnumeration init should work as expected"""
# should work for alphabet object
a = JointEnumeration([DnaBases, RnaBases])
self.assertEqual(len(a), 16)
self.assertEqual(a.shape, (4, 4))
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("G", "G"))
assert_equal(a._sub_enum_factors, array([[4], [1]]))
# should work for arbitrary sequences
a = JointEnumeration(["TCAG", "UCAG"])
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("G", "G"))
assert_equal(a._sub_enum_factors, array([[4], [1]]))
# should work for different length sequences
a = JointEnumeration(["TCA", "UCAG"])
self.assertEqual(a.shape, (3, 4))
self.assertEqual(len(a), 12)
self.assertEqual(a[0], ("T", "U"))
self.assertEqual(a[-1], ("A", "G"))
assert_equal(a._sub_enum_factors, array([[4],
[1]])) # note: _not_ [3,1]
def test_unpack_arrays(self):
"""JointEnumeration unpack_arrays should return correct arrays."""
a = JointEnumeration(["xyz", "abcd", "ef"])
v = [7, 15, 18, 0]
result = a.unpack_arrays(v)
self.assertEqual(result,
array([[0, 1, 2, 0], [3, 3, 1, 0], [1, 1, 0, 0]]))
def test_pack_arrays(self):
"""JointEnumeration pack_arrays should return correct array."""
a = JointEnumeration(["xyz", "abcd", "ef"])
v = [[0, 1, 2, 0], [3, 3, 1, 0], [1, 1, 0, 0]]
result = a.pack_arrays(v)
assert_equal(result, array([7, 15, 18, 0]))
def test_from_indices(self):
"""JointEnumeration from_indices should return correct tuples"""
a = JointEnumeration(["TCAG", "UCAG"])
i = a.from_indices([0, 15, 15])
self.assertEqual(i, [("T", "U"), ("G", "G"), ("G", "G")])
def test_to_indices(self):
"""JointEnumeration to_indices should convert tuples correctly"""
a = JointEnumeration(["TCAG", "UCAG"])
i = a.to_indices([("T", "U"), ("G", "G"), ("G", "G")])
self.assertEqual(i, [0, 15, 15])