def test7(self):
s1 = "CCCAAAAATTTAAAAACCCCCGGG"
s2 = "GGGAAAAAAAAAATTTCCCCCCCC"
S = self.S3
o = 5
c = 2
correct_score = 128
s, a1, a2 = alignment.SmithWatermanAffine(s1, s2, S, o, c)
self.assertEqual(alignment_util.scoreAlignmentAffine(a1,a2,S,o,c), s, "Returned alignment score does not match actual alignment score")
self.assertEqual(alignment_util.scoreAlignmentAffine(a1,a2,S,o,c), correct_score, "Score of returned alignment is not optimal")
def test3(self):
s1 = "AAAAAGTGAAAAA"
s2 = "AAAAACAAAAA"
S = self.S2
o = 2
c = 1
correct_score = 35
s, a1, a2 = alignment.SmithWatermanAffine(s1, s2, S, o, c)
self.assertEqual(alignment_util.scoreAlignmentAffine(a1,a2,S,o,c), s, "Returned alignment score does not match actual alignment score")
self.assertEqual(alignment_util.scoreAlignmentAffine(a1,a2,S,o,c), correct_score, "Score of returned alignment is not optimal")
def test7(self):
s1 = "CCCAAAAATTTAAAAACCCCCGGG"
s2 = "GGGAAAAAAAAAATTTCCCCCCCC"
S = self.S3
o = 5
c = 2
correct_score = 128
s, a1, a2 = alignment.SmithWatermanAffine(s1, s2, S, o, c)
self.assertEqual(
alignment_util.scoreAlignmentAffine(a1, a2, S, o, c), s,
"Returned alignment score does not match actual alignment score")
self.assertEqual(alignment_util.scoreAlignmentAffine(a1, a2, S, o,
c), correct_score,
"Score of returned alignment is not optimal")
def test3(self):
s1 = "AAAAAGTGAAAAA"
s2 = "AAAAACAAAAA"
S = self.S2
o = 2
c = 1
correct_score = 35
s, a1, a2 = alignment.SmithWatermanAffine(s1, s2, S, o, c)
self.assertEqual(
alignment_util.scoreAlignmentAffine(a1, a2, S, o, c), s,
"Returned alignment score does not match actual alignment score")
self.assertEqual(alignment_util.scoreAlignmentAffine(a1, a2, S, o,
c), correct_score,
"Score of returned alignment is not optimal")
def mcalliTest(self):
s1 = 'CCCCCCCCCAAAAAAAAAAAAAAAAAAATAAACCCCCCC'
s2 = 'CCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTCCCCCCC'
S = {x:{y:100*self.S2[x][y] for y in "ACGT"} for x in "ACGT"}
o = 500
c = 1
correct_score = 5462
s, a1, a2 = alignment.SmithWatermanAffine(s1, s2, S, o,c)
self.assertEqual(alignment_util.scoreAlignmentAffine(a1,a2,S,o,c), s, "Returned alignment score does not match actual alignment")
self.assertEqual(alignment_util.scoreAlignmentAffine(a1,a2,S,o,c), correct_score, "Score of returned alignment is not optimal")
t, b1, b2 = alignment.SmithWatermanAffine(s2, s1, S, o,c)
self.assertEqual(alignment_util.scoreAlignmentAffine(b1,b2,S,o,c), t, "Returned alignment score does not match actual alignment")
self.assertEqual(alignment_util.scoreAlignmentAffine(b1,b2,S,o,c), correct_score, "Score of returned alignment is not optimal")
def test_SWA(seq1, seq2, S, o, c):
s, a1, a2 = alignment.SmithWatermanAffine(seq1, seq2, S, o, c)
s_sol, a1_sol, a2_sol = alignment_sol.SmithWatermanAffine(seq1, seq2, S, o, c)
score = 0
# First: test that the function has returned has an optimal alignment
if alignment_util.scoreAlignmentAffine(a1, a2, S, o, c) == s_sol:
score += 70
# Second: test that the function has returned an optimal score
if s == s_sol:
score += 20
# Third: Test that the function has returned the correct score for the alignment
if alignment_util.scoreAlignmentAffine(a1, a2, S, o, c) == s:
score += 10
return score/100.0
def test_SWA(seq1, seq2, S, o, c):
s, a1, a2 = alignment.SmithWatermanAffine(seq1, seq2, S, o, c)
s_sol, a1_sol, a2_sol = alignment_sol.SmithWatermanAffine(
seq1, seq2, S, o, c)
score = 0
# First: test that the function has returned has an optimal alignment
if alignment_util.scoreAlignmentAffine(a1, a2, S, o, c) == s_sol:
score += 70
# Second: test that the function has returned an optimal score
if s == s_sol:
score += 20
# Third: Test that the function has returned the correct score for the alignment
if alignment_util.scoreAlignmentAffine(a1, a2, S, o, c) == s:
score += 10
return score / 100.0
def mcalliTest(self):
s1 = 'CCCCCCCCCAAAAAAAAAAAAAAAAAAATAAACCCCCCC'
s2 = 'CCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTCCCCCCC'
S = {x: {y: 100 * self.S2[x][y] for y in "ACGT"} for x in "ACGT"}
o = 500
c = 1
correct_score = 5462
s, a1, a2 = alignment.SmithWatermanAffine(s1, s2, S, o, c)
self.assertEqual(
alignment_util.scoreAlignmentAffine(a1, a2, S, o, c), s,
"Returned alignment score does not match actual alignment")
self.assertEqual(alignment_util.scoreAlignmentAffine(a1, a2, S, o,
c), correct_score,
"Score of returned alignment is not optimal")
t, b1, b2 = alignment.SmithWatermanAffine(s2, s1, S, o, c)
self.assertEqual(
alignment_util.scoreAlignmentAffine(b1, b2, S, o, c), t,
"Returned alignment score does not match actual alignment")
self.assertEqual(alignment_util.scoreAlignmentAffine(b1, b2, S, o,
c), correct_score,
"Score of returned alignment is not optimal")
