def test_complement(self):
"""Alphabet complement should correctly complement sequence"""
self.assertEqual(RnaAlphabet.complement('UauCG-NR'), 'AuaGC-NY')
self.assertEqual(DnaAlphabet.complement('TatCG-NR'), 'AtaGC-NY')
self.assertEqual(RnaAlphabet.complement(''), '')
self.assertRaises(TypeError, ProteinAlphabet.complement, 'ACD')
#if it wasn't a string, result should be a list
self.assertEqual(RnaAlphabet.complement(list('UauCG-NR')),
list('AuaGC-NY'))
self.assertEqual(RnaAlphabet.complement(('a','c')), ('u','g'))
#constructor should fail for a dict
self.assertRaises(ValueError, RnaAlphabet.complement, {'a':'c'})
def test_rc(self):
"""Alphabet rc should correctly reverse-complement sequence"""
self.assertEqual(RnaAlphabet.rc('UauCG-NR'), 'YN-CGauA')
self.assertEqual(DnaAlphabet.rc('TatCG-NR'), 'YN-CGatA')
self.assertEqual(RnaAlphabet.rc(''), '')
self.assertEqual(RnaAlphabet.rc('A'), 'U')
self.assertRaises(TypeError, ProteinAlphabet.rc, 'ACD')
#if it wasn't a string, result should be a list
self.assertEqual(RnaAlphabet.rc(list('UauCG-NR')),
list('YN-CGauA'))
self.assertEqual(RnaAlphabet.rc(('a','c')), ('g','u'))
#constructor should fail for a dict
self.assertRaises(ValueError, RnaAlphabet.rc, {'a':'c'})
def test_disambiguate(self):
"""Alphabet disambiguate should remove degenerate bases"""
d = RnaAlphabet.disambiguate
self.assertEqual(d(''), '')
self.assertEqual(d('AGCUGAUGUA--CAGU'),'AGCUGAUGUA--CAGU')
self.assertEqual(d('AUn-yrs-wkmCGwmrNMWRKY', 'strip'), 'AU--CG')
self.assertEqual(d(tuple('AUn-yrs-wkmCGwmrNMWRKY'), 'strip'), \
tuple('AU--CG'))
s = 'AUn-yrs-wkmCGwmrNMWRKY'
t = d(s, 'random')
u = d(s, 'random')
for i, j in zip(s, t):
if i in RnaAlphabet.Degenerates:
assert j in RnaAlphabet.Degenerates[i]
else:
assert i == j
self.assertNotEqual(t, u)
self.assertEqual(d(tuple('UCAG'), 'random'), tuple('UCAG'))
self.assertEqual(len(s), len(t))
assert RnaAlphabet.firstDegenerate(t) is None
#should raise exception on unknown disambiguation method
self.assertRaises(NotImplementedError, d, s, 'xyz')
