def local_test7(self): s1 = 'WCFFEXTSYRKFNTHPEQRNGDQSHITZBZYHBPEMKASGGZXACAYVHVNSLYXLFSNZNBIZRRANXYVNKBPAZVGEVMBACMTPQSDSFMFQMBKVCXDVYQBLACINNGLTTSYDSYFZTFYBR' s2 = 'CPDAZPXGMFLHMZZKKBMTPCDTXPLWKSEAGDQSHITZBZYHMKASGGZXACAYVHVNBZYCCSLYXLFSNZNBIZRRANXYVNFBPAZVGEVMBACMTPQSDSFMFQMBKVCFZBXDVYQBLACINKXDPXMYGY' S = self.S4 gap = 12 correct_score = 298 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), correct_score, "Score of returned alignment is not optimal")
def global_test2(self): s1 = "AAA" s2 = "AAA" S = self.S2 gap = 1 correct_score = 12 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), correct_score, "Score of returned alignment is not optimal")
def global_test7(self): s1 = 'GDQSHITZBZYHBPEMKASGGZXACAYVHVNSLYXLFSNZNBIZRRANXYVNKBPAZVGEVMBACMTPQSDSFMFQMBKVCXDVYQBLACIN' s2 = 'GDQSHITZBZYHMKASGGZXACAYVHVNBZYCCSLYXLFSNZNBIZRRANXYVNFBPAZVGEVMBACMTPQSDSFMFQMBKVCFZBXDVYQBLACIN' S = self.S4 gap = 5 correct_score = 375 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), correct_score, "Score of returned alignment is not optimal") s, a1, a2 = alignment.SmithWaterman(s2, s1, S, gap) self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), correct_score, "Score of returned alignment is not optimal")
def local_test6(self): s1 = "CCCCCACCCCC" s2 = "TTTCCCCCCCCCCTTT" S = self.S2 gap = 4 correct_score = 36 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), correct_score, "Score of returned alignment is not optimal") s, a1, a2 = alignment.SmithWaterman(s2, s1, S, gap) self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1,a2,S,gap), correct_score, "Score of returned alignment is not optimal")
def global_test2(self): s1 = "AAA" s2 = "AAA" S = self.S2 gap = 1 correct_score = 12 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual( alignment_util.scoreAlignment(a1, a2, S, gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1, a2, S, gap), correct_score, "Score of returned alignment is not optimal")
def local_test7(self): s1 = 'WCFFEXTSYRKFNTHPEQRNGDQSHITZBZYHBPEMKASGGZXACAYVHVNSLYXLFSNZNBIZRRANXYVNKBPAZVGEVMBACMTPQSDSFMFQMBKVCXDVYQBLACINNGLTTSYDSYFZTFYBR' s2 = 'CPDAZPXGMFLHMZZKKBMTPCDTXPLWKSEAGDQSHITZBZYHMKASGGZXACAYVHVNBZYCCSLYXLFSNZNBIZRRANXYVNFBPAZVGEVMBACMTPQSDSFMFQMBKVCFZBXDVYQBLACINKXDPXMYGY' S = self.S4 gap = 12 correct_score = 298 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual( alignment_util.scoreAlignment(a1, a2, S, gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1, a2, S, gap), correct_score, "Score of returned alignment is not optimal")
def test_SW(seq1, seq2, S, g): s, a1, a2 = alignment.SmithWaterman(seq1, seq2, S, g) s_sol, a1_sol, a2_sol = alignment_sol.SmithWaterman(seq1, seq2, S, g) score = 0 # First: test that the function has returned has an optimal alignment if alignment_util.scoreAlignment(a1, a2, S, g) == 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.scoreAlignment(a1, a2, S, g) == s: score += 10 return score/100.0
def test_SW(seq1, seq2, S, g): s, a1, a2 = alignment.SmithWaterman(seq1, seq2, S, g) s_sol, a1_sol, a2_sol = alignment_sol.SmithWaterman(seq1, seq2, S, g) score = 0 # First: test that the function has returned has an optimal alignment if alignment_util.scoreAlignment(a1, a2, S, g) == 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.scoreAlignment(a1, a2, S, g) == s: score += 10 return score / 100.0
def local_test6(self): s1 = "CCCCCACCCCC" s2 = "TTTCCCCCCCCCCTTT" S = self.S2 gap = 4 correct_score = 36 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual( alignment_util.scoreAlignment(a1, a2, S, gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1, a2, S, gap), correct_score, "Score of returned alignment is not optimal") s, a1, a2 = alignment.SmithWaterman(s2, s1, S, gap) self.assertEqual( alignment_util.scoreAlignment(a1, a2, S, gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1, a2, S, gap), correct_score, "Score of returned alignment is not optimal")
def global_test7(self): s1 = 'GDQSHITZBZYHBPEMKASGGZXACAYVHVNSLYXLFSNZNBIZRRANXYVNKBPAZVGEVMBACMTPQSDSFMFQMBKVCXDVYQBLACIN' s2 = 'GDQSHITZBZYHMKASGGZXACAYVHVNBZYCCSLYXLFSNZNBIZRRANXYVNFBPAZVGEVMBACMTPQSDSFMFQMBKVCFZBXDVYQBLACIN' S = self.S4 gap = 5 correct_score = 375 s, a1, a2 = alignment.SmithWaterman(s1, s2, S, gap) self.assertEqual( alignment_util.scoreAlignment(a1, a2, S, gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1, a2, S, gap), correct_score, "Score of returned alignment is not optimal") s, a1, a2 = alignment.SmithWaterman(s2, s1, S, gap) self.assertEqual( alignment_util.scoreAlignment(a1, a2, S, gap), s, "Returned alignment score does not match actual alignment score") self.assertEqual(alignment_util.scoreAlignment(a1, a2, S, gap), correct_score, "Score of returned alignment is not optimal")