def test_check_number_less_saved_paths(tmpdir):
path = tmpdir.join("output.txt")
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=1, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
_, saved_paths = gc.run_save(seq1, seq2, path)
assert saved_paths == 1
def test_init_graph_nodes():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
_, G = gc._initialize_structures(seq1, seq2)
assert list(G.nodes()) == [(0, 0), (1, 0), (2, 0), (3, 0), (4, 0), (0, 1),
(0, 2), (0, 3), (0, 4), (0, 5)]
def test_high_penalty_gap(tmpdir):
path = tmpdir.join("output.txt")
gc = GenomCompare(same=5, diff=-5, gp=-10, max_paths=100, max_seq_len=100)
seq1 = 'SAM'
seq2 = 'SUM'
_ = gc.run_save(seq1, seq2, path)
with open(path) as f:
assert f.read() == 'SCORE = 5\n\nSAM\nSUM\n'
def test_check_saving_less_paths(tmpdir):
path = tmpdir.join("output.txt")
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=1, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
_ = gc.run_save(seq1, seq2, path)
with open(path) as f:
assert f.read() == 'SCORE = 9\n\n-MAR-S\nSMART-\n'
def test_too_long_seq2():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=4)
seq1 = 'MARS'
seq2 = 'SMART'
with pytest.raises(InvalidSeqLengthError):
gc.run(seq1, seq2)
########### MORE COMPLICATED EXAMPLES ################
def test_simple_value_after_order_switch():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
m, _ = gc.run(seq1, seq2)
v1 = m[-1, -1]
m, _ = gc.run(seq2, seq1)
v2 = m[-1, -1]
assert v1 == v2
def test_simple_matrix_values():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
m, _ = gc.run(seq1, seq2)
assert np.array_equal(
m,
np.array([[0, -2, -4, -6, -8, -10], [-2, -4, 3, 1, -1, -3],
[-4, -6, 1, 8, 6, 4], [-6, -8, -1, 6, 13, 11],
[-8, -1, -3, 4, 11, 9]]))
def test_init_matrix_values():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
matrix, _ = gc._initialize_structures(seq1, seq2)
assert np.array_equal(
matrix,
np.array([[0, -2, -4, -6, -8, -10], [-2, 0, 0, 0, 0, 0],
[-4, 0, 0, 0, 0, 0], [-6, 0, 0, 0, 0, 0],
[-8, 0, 0, 0, 0, 0]]))
def test_simple_graph_edges():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
_, G = gc.run(seq1, seq2)
assert list(G.edges()) == [((1, 0), (0, 0)), ((2, 0), (1, 0)),
((3, 0), (2, 0)), ((4, 0), (3, 0)),
((0, 1), (0, 0)), ((0, 2), (0, 1)),
((0, 3), (0, 2)), ((0, 4), (0, 3)),
((0, 5), (0, 4)), ((1, 1), (0, 1)),
((1, 1), (1, 0)), ((1, 2), (0, 1)),
((1, 3), (1, 2)), ((1, 4), (1, 3)),
((1, 5), (1, 4)), ((2, 1), (1, 1)),
((2, 1), (2, 0)), ((2, 2), (1, 2)),
((2, 3), (1, 2)), ((2, 4), (2, 3)),
((2, 5), (2, 4)), ((3, 1), (2, 1)),
((3, 1), (3, 0)), ((3, 2), (2, 2)),
((3, 3), (2, 3)), ((3, 4), (2, 3)),
((3, 5), (3, 4)), ((4, 1), (3, 0)),
((4, 2), (3, 2)), ((4, 2), (4, 1)),
((4, 3), (3, 3)), ((4, 4), (3, 4)),
((4, 5), (3, 5)), ((4, 5), (4, 4))]
def test_simple_graph_nodes():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
_, G = gc.run(seq1, seq2)
assert set(G.nodes()) == set(itertools.product(range(5), range(6)))
def test_simple_final_score():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
m, _ = gc.run(seq1, seq2)
assert m[-1, -1] == 9
def test_init_matrix_size():
gc = GenomCompare(same=5, diff=-5, gp=-2, max_paths=100, max_seq_len=100)
seq1 = 'MARS'
seq2 = 'SMART'
matrix, _ = gc._initialize_structures(seq1, seq2)
assert matrix.shape == (5, 6)
parser.add_argument('-c', dest='config_path', required=True, help='path to config file')
parser.add_argument('-o', dest='output_path', required=True, help='path to output file')
args = parser.parse_args()
return args
if __name__ == '__main__':
args = parse_args()
parser = ConfigParser()
try:
config = parser.load_config(args.config_path)
except (json.JSONDecodeError, ConfigError) as e:
logging.error(e)
sys.exit(1)
comparer = GenomCompare(same=config['SAME'], diff=config['DIFF'], gp=config['GP'], \
max_paths=config['MAX_NUMBER_PATHS'], max_seq_len=config['MAX_SEQ_LENGTH'])
seq1 = load_fasta(args.seq1_path)
seq2 = load_fasta(args.seq2_path)
try:
score, saved_paths = comparer.run_save(seq1, seq2, 'tmp.txt')
except InvalidSeqLengthError as e:
logging.error(e)
sys.exit(1)
print(f'Score: {score}\nPaths written: {saved_paths}')