def test_get_mutations(self):
'''Tests get_mutations method.'''
wt_seq = 'QWERTY'
mt_seq = 'QTER-Y'
mut_a = mut_utils.Mutation('W', 2, 'T')
mut_b = mut_utils.Mutation('T', 5, '-')
mut_lst = [mut_a, mut_b]
self.assertEqual(mut_utils.get_mutations(wt_seq, mt_seq), mut_lst)
def test_parse_mut_str(self):
'''Tests parse_mut_str method.'''
mut_a = mut_utils.Mutation('A', 12, 'V')
mut_b = mut_utils.Mutation('P', 5, '-')
mut_lst = [mut_a, mut_b]
mut_str = ' '.join([str(mut) for mut in mut_lst])
self.assertEqual(mut_str, 'A12V P5-')
self.assertEqual(mut_utils.parse_mut_str(mut_str), mut_lst)
def test_cmp(self):
'''Tests __cmp__.'''
mut_a = mut_utils.Mutation('A', 12, 'V')
mut_b = mut_utils.Mutation('A', 5, 'V')
mut_c = mut_utils.Mutation('A', 12, 'T')
lst = [mut_a, mut_b, mut_c]
sort_lst = [mut_b, mut_c, mut_a]
self.assertNotEqual(lst, sorted(lst))
self.assertEqual(sort_lst, sorted(lst))
def test_eq(self):
'''Tests __eq__.'''
mut_a = mut_utils.Mutation('A', 12, 'V')
mut_b = mut_utils.Mutation('A', 12, 'V')
mut_c = mut_utils.Mutation('A', 13, 'V')
mut_d = mut_utils.Mutation('A', 12, 'T')
self.assertEqual(mut_a, mut_b)
self.assertNotEqual(mut_a, mut_c)
self.assertNotEqual(mut_a, mut_d)
def test_apply_mutations(self):
'''Tests apply_mutations method.'''
aa_len = 1024
wt_seq = [random.choice(list(seq_utils.AA_CODES.values()))
for _ in range(aa_len)]
mt_seq = list(wt_seq)
mutations = []
for _ in range(16):
pos = random.randint(0, aa_len)
wt_res = wt_seq[pos]
aa_codes = list(seq_utils.AA_CODES.values())
aa_codes.remove('*')
mt_res = random.choice(aa_codes)
mt_seq[pos] = mt_res
mutations.append(mut_utils.Mutation(wt_res, pos + 1, mt_res))
self.assertEqual(mut_utils.apply_mutations(wt_seq, mutations),
''.join(mt_seq))
def test_str(self):
'''Tests __str__.'''
mut = mut_utils.Mutation('A', 12, 'V')
self.assertEqual(mut.__str__(), 'A12V')
def test_repr(self):
'''Tests __repr__.'''
mut = mut_utils.Mutation('A', 12, '-')
self.assertEqual(mut.__repr__(), 'A12-')