def test_single_character_match(self):
seq = 'A'
al_1, al_2, s = make_alignment(seq, seq, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq, seq)
self.assertEqual(seq, al_1)
self.assertEqual(seq, al_2)
self.assertEqual(MATCH, s)
def test_empty(self):
seq = ''
al_1, al_2, s = make_alignment(seq, seq, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq, seq)
self.assertEqual(seq, al_1)
self.assertEqual(seq, al_2)
self.assertEqual(0, s)
def test_match_mismatch(self):
seq1 = 'AT'
seq2 = 'AG'
al_1, al_2, s = make_alignment(seq1, seq2, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq1, seq2)
self.assertEqual(seq1, al_1)
self.assertEqual(seq2, al_2)
self.assertEqual(MATCH + MISMATCH, s)
def test_match_gap(self):
seq1 = 'A'
seq2 = 'AG'
al_1, al_2, s = make_alignment(seq1, seq2, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq1, seq2)
self.assertEqual('A-', al_1)
self.assertEqual('AG', al_2)
self.assertEqual(MATCH + GAP, s)
def test_single_character_mismatch(self):
seq1 = 'A'
seq2 = 'B'
al_1, al_2, s = make_alignment(seq1, seq2, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq1, seq2)
self.assertEqual(seq1, al_1)
self.assertEqual(seq2, al_2)
self.assertEqual(MISMATCH, s)
def test_shifted(self):
seq1 = 'ATG'
seq2 = 'GAT'
al_1, al_2, s = make_alignment(seq1, seq2, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq1, seq2)
self.assertEqual('-ATG', al_1)
self.assertEqual('GAT-', al_2)
self.assertEqual(2 * MATCH + 2 * GAP, s)
def test_border_flip(self):
seq1 = 'TGGGTA'
seq2 = 'A'
al_1, al_2, s = make_alignment(seq1, seq2, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, seq1, seq2)
self.assertEqual(seq1, al_1)
self.assertEqual('-----A', al_2)
self.assertEqual(MATCH + 5 * GAP, s)
def test_complex_2(self):
s_1WFN = 'GSSGSSGPQLVRTHEDVPGPVGHLSFSEILDTSLKVSWQEPGEKNGILTGYRISWEEYNRTNTRVTHYLPNVTLEYRVTGLTALTTYTIEVAAMTSKGQGQVSASTISSGVPPSGPSSG'
s_1WIS = 'GSSGSSGTISSGVPPELPGPPTNLGISNIGPRSVTLQFRPGYDGKTSISRWLVEAQVGVVGEGEEWLLIHQLSNEPDARSMEVPDLNPFTCYSFRMRQVNIVGTSPPSQPSRKIQTLQSGPSSG'
al_1, al_2, s = make_alignment(s_1WFN, s_1WIS, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, s_1WFN, s_1WIS)
self.assertEqual(-27, s)
def test_complex_1(self):
s_1WFN = 'GSSGSSGPQLVRTHEDVPGPVGHLSFSEILDTSLKVSWQEPGEKNGILTGYRISWEEYNRTNTRVTHYLPNVTLEYRVTGLTALTTYTIEVAAMTSKGQGQVSASTISSGVPPSGPSSG'
s_1WFO = 'GSSGSSGRIGDGSPSHPPILERTLDDVPGPPMGILFPEVRTTSVRLIWQPPAAPNGIILAYQITHRLNTTTANTATVEVLAPSARQYTATGLKPESVYLFRITAQTRKGWGEAAEALVVTTEKRSGPSSG'
al_1, al_2, s = make_alignment(s_1WFN, s_1WFO, MATCH, MISMATCH, GAP)
self.check_answer_correctness(al_1, al_2, s, s_1WFN, s_1WFO)
self.assertEqual(6, s)