def test_isValid(self):
"""Enumeration isValid should return True for valid sequence"""
a = Enumeration('bca')
self.assertEqual(a.isValid(''), True)
self.assertEqual(a.isValid('bbb'), True)
self.assertEqual(a.isValid('bbbaac'), True)
self.assertEqual(a.isValid('bbd'), False)
self.assertEqual(a.isValid('d'), False)
self.assertEqual(a.isValid(['a', 'b']), True)
self.assertEqual(a.isValid(['a', None]), False)
def test_isValid(self):
"""Enumeration isValid should return True for valid sequence"""
a = Enumeration('bca')
self.assertEqual(a.isValid(''), True)
self.assertEqual(a.isValid('bbb'), True)
self.assertEqual(a.isValid('bbbaac'), True)
self.assertEqual(a.isValid('bbd'), False)
self.assertEqual(a.isValid('d'), False)
self.assertEqual(a.isValid(['a', 'b']), True)
self.assertEqual(a.isValid(['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.GapIndex, 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.ArrayType, 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.GapIndex, 13)
self.assertEqual(b.ArrayType, uint8)
#check that array type is set correctly if needed
b = a**6 #too big to fit in char
self.assertEqual(b.ArrayType, uint16)
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)
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.ArrayType, 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.GapIndex, 2)
a = Enumeration(range(257)) #too big to fit in uint8
self.assertEqual(a.ArrayType, uint16)
def test_fromIndices(self):
"""Enumeration fromIndices should return elements from indices"""
a = Enumeration('bca')
self.assertEqual(a.fromIndices([]), [])
self.assertEqual(a.fromIndices([1,1,2,0,2,1]), list('ccabac'))
def test_toIndices(self):
"""Enumeration toIndices should return indices from elements"""
a = Enumeration('bca')
self.assertEqual(a.toIndices(''), [])
self.assertEqual(a.toIndices('ccabac'), [1,1,2,0,2,1])
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)
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.ArrayType, 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.GapIndex, 2)
a = Enumeration(range(257)) #too big to fit in uint8
self.assertEqual(a.ArrayType, uint16)
def test_fromIndices(self):
"""Enumeration fromIndices should return elements from indices"""
a = Enumeration('bca')
self.assertEqual(a.fromIndices([]), [])
self.assertEqual(a.fromIndices([1,1,2,0,2,1]), list('ccabac'))
def test_toIndices(self):
"""Enumeration toIndices should return indices from elements"""
a = Enumeration('bca')
self.assertEqual(a.toIndices(''), [])
self.assertEqual(a.toIndices('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')