def nw_verbose(seq1, seq2, cost_table=None, cost_mat=None, key=None, timer=1):
'''
Animated the needleman algorithm, on each iteration it clears the terminal, print the table and the path taken then wait for a specific amount
of time
Args:
seq1: the first sequence to align
seq2: the second sequence to align
cost_table: contains the match, mismatch and the gap cost in this order (mutual exlusive with cost_mat)
cost_mat: contains the cost matrix and the gap at the end (mutual exlusive with cost_table and used with key)
key: the order of the letters in the cost matrix (mutual exlusive with cost_table)
timer: timer to sleep on each iteration
Returns:
None
'''
alg, alg_mat, path = needleman(seq1,
seq2,
cost_table=cost_table,
cost_mat=cost_mat,
key=key,
verbose=True)
alg.append(create_aligner_str(alg[0], alg[1]))
path.append((-1, -1))
seen = []
for coord in path:
clear()
print_nw_table(seq1, seq2, alg, alg_mat, coord, seen)
seen.append(coord)
sleep(timer)
def test_needlman_mat():
for t in TEST_CASES_MAT:
#----------- Our Implementation -----------
m1 = needleman(t[0], t[1], cost_mat=t[2], key=t[3])
#---------------- Bio Seq ----------------
m2 = nw_bio_mat(t[0], t[1], cost_mat=t[2], key=t[3])
#------------------ Test ------------------
assert m1 in m2
def test_needlman():
for t in TEST_CASES_NORMAL:
#----------- Our Implementation -----------
m = needleman(t[0], t[1], t[2])
#---------------- Bio Seq -----------------
m2 = nw_bio(t[0], t[1], t[2])
#------------------ Test ------------------
assert m in m2
def test_needleman_random_gen():
for _ in range(0, EPOCHS) :
#----------- Generating random arguments -----------
cost_table = [ random.randint(-10, 10), random.randint(-10, 0), random.randint(-10, 0) ]
args = arg_generator(N=NW_RUNS, stride=1, type=STRINGS, variant_arg_pos=[0, 1], static_args=[cost_table], start=1,
same_size=False, lower=(NW_RUNS//2)+1, upper=NW_RUNS)
for arg in args:
#------------------ Test ------------------
assert needleman(*arg) in nw_bio_generic(*arg)
def test_needleman_mat_random_gen():
for i in range(0, EPOCHS) :
#----------- Generating random arguments -----------
key = ''.join(list(set(random.choices(string.ascii_lowercase, k=i+2))))
cost_mat = [ random.randint(-10, 10) for _ in range(len(key) ** 2 + 1) ]
args = arg_generator(N=NW_RUNS, stride=1, type=STRINGS, samples=key, variant_arg_pos=[0, 1], static_args=[None, cost_mat, key],
start=1, same_size=False, lower=(NW_RUNS//2)+1, upper=NW_RUNS)
for arg in args:
#------------------ Test ------------------
assert needleman(*arg) in nw_bio_generic(*arg)