def test_compute_cost_matrix_simple():
config = utils.Config(5, -5, -2, 99, 9999)
a = "SAM"
b = "SUM"
algo_instance = algo.NWAlgo(config)
cost_matrix = algo_instance.compute_cost_matrix(a, b)
assert cost_matrix[len(a), len(b)] == 6
def test_compute_cost_matrix_advanced():
config = utils.Config(5, -5, -2, 99, 9999)
a = "GAAC"
b = "CAAGAC"
algo_instance = algo.NWAlgo(config)
cost_matrix = algo_instance.compute_cost_matrix(a, b)
assert cost_matrix[len(a), len(b)] == 7
def test_get_all_alignments():
config = utils.Config(5, -5, -2, 99, 9999)
a = "SAM"
b = "SUM"
algo_instance = algo.NWAlgo(config)
cost_matrix = algo_instance.compute_cost_matrix(a, b)
alignments = algo_instance.get_all_alignments(a, b, cost_matrix)
assert alignments == [("SA-M", "S-UM"), ("S-AM", "SU-M")]
def test_retrieve_previous_nodes():
config = utils.Config(5, -5, -2, 99, 9999)
a = "SAM"
b = "SUM"
algo_instance = algo.NWAlgo(config)
cost_matrix = algo_instance.compute_cost_matrix(a, b)
graph = algo_instance._retrieve_previous_nodes(a, b, cost_matrix)
assert graph[(3, 2)] == [(3, 1), (2, 2)]
def test_find_all_paths_truncated():
config = utils.Config(5, -5, -2, 1, 9999)
a = "SAM"
b = "SUM"
algo_instance = algo.NWAlgo(config)
cost_matrix = algo_instance.compute_cost_matrix(a, b)
graph = algo_instance._retrieve_previous_nodes(a, b, cost_matrix)
paths = algo_instance._find_all_paths(graph, (len(a), len(b)), (0, 0),
list())
assert paths == [
[(3, 3), (2, 2), (2, 1), (1, 1), (0, 0)],
]