def test_qxalign_simple():
q = Qxalign()
q.prepare("AAAACGT", "TGCA", "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
assert 60 == q.align()
del q
def test_qualityScores(self):
q = Qxalign()
q.prepare("AAAACGT", "TGCA", "!!!!!!!!!!!")
self.assertEqual(60, q.align())
def test_qxalign_long():
q = Qxalign()
q.prepare("AAAACGT", "TGCA", b"!!!!")
assert 60 == q.align()
q.trace()
assert "3I 1=" == q.show_trace()
q.prepare_query(query_seq="CAAC")
assert 40 == q.align(semi=True)
q.trace()
assert "1X 3=" == q.show_trace()
q.prepare("", "", "")
try:
q.align()
except IndexError:
pass
else:
assert False
del q
def test_qualityScoresTrace(self):
q = Qxalign()
q.prepare("AAAACGT", "TGCA", b"!!!!")
self.assertEqual(60, q.align())
q.trace()
self.assertEqual("3I 1=", q.show_trace())
q.prepare_query(query_seq="CAAC")
self.assertEqual(40, q.align(semi=True))
q.trace()
self.assertEqual("1X 3=", q.show_trace())
q.prepare("", "", "")
self.assertRaises(IndexError, q.align, [])