class AlignmentPathsTests(unittest.TestCase):
def setUp(self):
self.solver = NeedlemanWunschSolver(
CellCostComputer(same_cost=5, diff_cost=-5, gap_penalty=-2))
@parameterized.expand(
[[0, {("", "")}, "", ""], [5, {("A", "A")}, "A", "A"],
[3, {("AA", "A-"), ("AA", "-A")}, "AA", "A"],
[1, {("A-S", "AA-"), ("-AS", "AA-"), ("AS-", "A-A")}, "AS", "AA"],
[
-3,
{("AAA-D", "--AS-"), ("A-AAD", "AS---"), ("AA-AD", "A-S--"),
("AAA-D", "A--S-"), ("AA-AD", "-AS--"), ("AAAD-", "A---S"),
("AAAD-", "--A-S"), ("AAAD-", "-A--S"), ("AAA-D", "-A-S-")},
"AAAD", "AS"
], [-8, {("----", "AAAD")}, "", "AAAD"],
[
-10,
{("AAAD-", "----S"), ("AA-AD", "--S--"), ("AAA-D", "---S-"),
("-AAAD", "S----"), ("A-AAD", "-S---")}, "AAAD", "S"
], [6, {("ABCD", "A--D")}, "ABCD", "AD"]])
def test(self, expected_score, expected_alignments, seq_a, seq_b):
score, alignment = self.solver.generate_alignments(a_seq=seq_a,
b_seq=seq_b)
self.assertSetEqual(alignment, expected_alignments)
self.assertEqual(score, expected_score)
def test_max_paths_if_there_are_more_possible(self):
self.__check_max_paths(2)
def test_max_paths_if_there_are_less_possible(self):
self.__check_max_paths(100)
def test_max_paths_is_0_then_no_alignment(self):
self.__check_max_paths(0)
def __check_max_paths(self, max_paths):
_, alignment = self.solver.generate_alignments("AADD", "S", max_paths)
self.assertTrue(len(alignment) <= max_paths)
def get_alignments(config: Dict[str, int], seq_a: str, seq_b: str):
solver = NeedlemanWunschSolver(
CellCostComputer(same_cost=config["SAME"],
diff_cost=config["DIFF"],
gap_penalty=config["GAP_PENALTY"]))
return solver.generate_alignments(seq_a, seq_b, config["MAX_NUMBER_PATHS"])