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'))
self.assertEqual(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'))
self.assertEqual(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'))
self.assertEqual(a._sub_enum_factors, \
array([[4],[1]])) #note: _not_ [3,1]
def test_unpackArrays(self):
"""JointEnumeration unpackArrays should return correct arrays."""
a = JointEnumeration(['xyz', 'abcd', 'ef'])
v = [7, 15, 18, 0]
result = a.unpackArrays(v)
self.assertEqual(result,
array([[0, 1, 2, 0], [3, 3, 1, 0], [1, 1, 0, 0]]))
def test_unpackArrays(self):
"""JointEnumeration unpackArrays should return correct arrays."""
a = JointEnumeration(['xyz', 'abcd', 'ef'])
v = [7,15,18,0]
result = a.unpackArrays(v)
self.assertEqual(result, array([[0,1,2,0],[3,3,1,0], [1,1,0,0]]))
def test_fromIndices(self):
"""JointEnumeration fromIndices should return correct tuples"""
a = JointEnumeration(['TCAG','UCAG'])
i = a.fromIndices([0, 15, 15])
self.assertEqual(i, [('T','U'),('G','G'),('G','G')])
def test_toIndices(self):
"""JointEnumeration toIndices should convert tuples correctly"""
a = JointEnumeration(['TCAG','UCAG'])
i = a.toIndices([('T','U'),('G','G'),('G','G')])
self.assertEqual(i, [0, 15, 15])
def test_fromIndices(self):
"""JointEnumeration fromIndices should return correct tuples"""
a = JointEnumeration(['TCAG','UCAG'])
i = a.fromIndices([0, 15, 15])
self.assertEqual(i, [('T','U'),('G','G'),('G','G')])
def test_toIndices(self):
"""JointEnumeration toIndices should convert tuples correctly"""
a = JointEnumeration(['TCAG','UCAG'])
i = a.toIndices([('T','U'),('G','G'),('G','G')])
self.assertEqual(i, [0, 15, 15])
