def test_align___0(self):
# initialize SequencePair
sp = pairwise.SequencePair("", "")
# call align function with specific input
self.assertTrue(
sp.align("AAA", "GAAAGGG", open_penalty=3,
extend_penalty=3).traceback.query == '-AAA---')
def test_SequencePair___returns_hamming_distance0_5(self):
self.assertTrue(
pairwise.SequencePair("AAAAAAAAAA", "AAAAA").hamming_distance ==
5.0)
def test_SequencePair___returns_hamming_distance0_083(self):
self.assertTrue(
pairwise.SequencePair("CAGQASQGNLIF",
"CAGQRSQGNLIF").hamming_distance == 1.0)
def test_SequencePair___leninput2_lt_5_returns_distance_None(self):
self.assertTrue(
pairwise.SequencePair("CAGQASQGNLIF", "CAGA").hamming_distance ==
None)
def test_SequencePair___returns_TypeError(self):
with self.assertRaises(TypeError):
pairwise.SequencePair("CAGQASQGNLIF", 1)
def test_align___2(self):
self.assertTrue(
pairwise.SequencePair("AACAGQASQGNLIF", "CAGQASQGNLIF").a2 ==
'--CAGQASQGNLIF')
def my_distance_wrapper(a, b):
return (float(pairwise.SequencePair(a, b).hamming_distance))