A = line
while (A[-1] in ['\n', '\r']):
A = A[:-1]
B = f.readline()
while (B[-1] in ['\n', '\r']):
B = B[:-1]
f.readline()
line = f.readline()
# Run the NW algorithm
print("First sequence:", A)
print("Second sequence:", B)
print("Calculating alignment distance by Needleman-Wunsch method...")
z = nw(A, B, simMatrix, gapPenalty, alphEnum)
print("Alignment of A: ", z[0])
print("Alignment of B: ", z[1])
print("Similarity score: ", z[2], '\n')
# Write outputs to text file
g.write(str(z[2]) + "\n")
g.write(z[0] + "\n")
g.write(z[1] + "\n")
g.write("\n")
# Close the files and finish
f.close()
g.close()
random.seed()
# Number of trials
trials = 1000
print "Testing..."
for t in range(trials):
fail = False
n = random.randint(5, 100)
k = random.randint(1, n)
parent = ""
for i in range(n):
parent = parent + random.choice(alphabet)
child, work = mutate(parent, k)
nwout = nw(parent, child, simMatrix, gapPenalty, alphEnum)
hbout = hirschberg(parent, child, simMatrix, gapPenalty, alphEnum)
#Verification tests
compress = nwout[0].replace('-', '')
if compress != parent:
fail = True
compress = nwout[1].replace('-', '')
if compress != child:
fail = True
compress = hbout[0].replace('-', '')
if compress != parent:
fail = True
compress = hbout[1].replace('-', '')
if compress != child:
fail = True
trials = 100
repeats = 5
table = []
for t in range(trials):
n = random.randint(1, 1001)
m = random.randint(1, 1001)
A = B = ""
for i in range(n):
A += random.choice(alphabet)
for j in range(m):
B += random.choice(alphabet)
# Time the nw routine
t0 = time.clock()
for k in range(repeats):
nwout = nw(A, B, simMatrix, gapPenalty, alphEnum)
t1 = time.clock()
nwtime = (t1 - t0)/repeats
# Time the hirschberg routine
t0 = time.clock()
for k in range(repeats):
hbout = hirschberg(A, B, simMatrix, gapPenalty, alphEnum)
t1 = time.clock()
hbtime = (t1 - t0)/repeats
table.append([n, m, n*m, nwtime, hbtime])
print table[-1]
random.seed()
# Number of trials
trials = 1000
print "Testing..."
for t in range(trials):
fail = False
n = random.randint(5, 100)
k = random.randint(1, n)
parent = ""
for i in range(n):
parent = parent + random.choice(alphabet)
child, work = mutate(parent, k)
nwout = nw(parent, child, simMatrix, gapPenalty, alphEnum)
hbout = hirschberg(parent, child, simMatrix, gapPenalty, alphEnum)
#Verification tests
compress = nwout[0].replace('-', '')
if compress != parent:
fail = True
compress = nwout[1].replace('-', '')
if compress != child:
fail = True
compress = hbout[0].replace('-', '')
if compress != parent:
fail = True
compress = hbout[1].replace('-', '')
if compress != child:
fail = True