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Usage: align <input file> Error in python

Code implements the dynamic programming solution for global pairwise alignment of two sequences. Trying to perform a semi-global alignment between the SARS-CoV-2 reference genome and the first read in the Nanopore sample. The length of the reference genome is 29903 base pairs and the length of the first Nanopore read is 1246 base pairs. When I run the following code, I get this message in my terminal:
import sys
import numpy as np
GAP = -2
MATCH = 5
MISMATCH = -3
MAXLENGTH_A = 29904
MAXLENGTH_B = 1247
# insert sequence files
A = open("SARS-CoV-2 reference genome.txt", "r")
B = open("Nanopore.txt", "r")
def max(A, B, C):
if (A >= B and A >= C):
return A
elif (B >= A and B >= C):
return B
else:
return C
def Tmax(A, B, C):
if (A > B and A > C):
return 'D'
elif (B > A and B > C):
return 'L'
else:
return 'U'
def m(p, q):
if (p == q):
return MATCH
else:
return MISMATCH
def append(st, c):
return c + "".join(i for i in st)
if __name__ == "__main__":
if (len(sys.argv) != 2):
print("Usage: align <input file>")
sys.exit()
if (not os.path.isfile(sys.argv[1])):
print("input file not found.")
sys.exit()
S = np.empty([MAXLENGTH_A, MAXLENGTH_B], dtype = int)
T = np.empty([MAXLENGTH_A, MAXLENGTH_B], dtype = str)
with open(sys.argv[1], "r") as file:
A = str(A.readline())[:-1]
B = str(B.readline())[:-1]
print("Sequence A:",A)
print("Sequence B:",B)
N = len(A)
M = len(B)
S[0][0] = 0
T[0][0] = 'D'
for i in range(0, N + 1):
S[i][0] = GAP * i
T[i][0] = 'U'
for i in range(0, M + 1):
S[0][i] = GAP * i
T[0][i] = 'L'
for i in range(1, N + 1):
for j in range(1, M + 1):
S[i][j] = max(S[i-1][j-1]+m(A[i-1],B[j-1]),S[i][j-1]+GAP,S[i-1][j]+GAP)
T[i][j] = Tmax(S[i-1][j-1]+m(A[i-1],B[j-1]),S[i][j-1]+GAP,S[i-1][j]+GAP)
print("The score of the alignment is :",S[N][M])
i, j = N, M
RA = RB = RM = ""
while (i != 0 or j != 0):
if (T[i][j]=='D'):
RA = append(RA,A[i-1])
RB = append(RB,B[j-1])
if (A[i-1] == B[j-1]):
RM = append(RM,'|')
else:
RM = append(RM,'*')
i -= 1
j -= 1
elif (T[i][j]=='L'):
RA = append(RA,'-')
RB = append(RB,B[j-1])
RM = append(RM,' ')
j -= 1
elif (T[i][j]=='U'):
RA = append(RA,A[i-1])
RB = append(RB,'-')
RM = append(RM,' ')
i -= 1
print(RA)
print(RM)
print(RB)

This has nothing to do with python. The error message comes this line:
if (len(sys.argv) != 2):
print("Usage: align <input file>")
The code expects to be called with exactly one argument, the input file:
align path/to/input/file
You provided a different number of arguments, probably zero.

Function not returning boolean [duplicate]

This question already has answers here:
Why Python recursive function returns None [duplicate]
(1 answer)
Recursive function does not return specified value
(2 answers)
Closed 1 year ago.
I have written a maze solver program. I want the PathFinder function to return True if a path is found and then print the path or else simply return False. But my program always keeps returning False even if a path is found. It would be great if you guys can help me figure this out.
def findPaths(m,path,i,j):
r,c = len(m), len(m[0])
if i == r-1 and j == c-1:
print(path)
return True
#explore
path.append(m[i][j])
# move down
if i != r-1 and m[i+1][j] == '↓ ':
findPaths(m,path,i+2,j)
#move up
if i < 0 and m[i-1][j] == '↑ ':
findPaths(m,path,i-2,j)
#move right
if j != c-1 and m[i][j+1] == '→':
findPaths(m,path,i,j+2)
#move left
if j > 0 and m[i][j-1] == '←':
findPaths(m,path,i,j-2)
path.pop()
def maze(r,c):
m = []
for i in range(r):
row = []
for j in range(1, c + (c)):
rand_num = str(randint(1, 99))
if j % 2 != 0:
if len(rand_num) == 1:
row.append(' ' + rand_num)
else:
row.append(rand_num)
else:
row.append('?')
m.append(row)
up_left_count = r * c // 3
down_right_count = r * c * 2 // 3
for v in range(r + (r - 1)):
vertical_lst = []
for each in range(1, c + c):
if each % 2 == 0:
vertical_lst.append(' ')
else:
vertical_lst.append('? ')
if v % 2 != 0:
m.insert(v, vertical_lst)
idx_i = []
idx_j = []
idx_v_i = []
idx_v_j = []
for i in range(len(m)):
for j in range(len(m[0])):
if i % 2 == 0 and j % 2 != 0:
idx_i.append(i)
idx_j.append(j)
for v_i in range(len(m)):
for v_j in range(len(m[0])):
if v_i % 2 != 0 and v_j % 2 == 0:
idx_v_i.append(v_i)
idx_v_j.append(v_j)
idx_i = list(set(idx_i))
idx_j = list(set(idx_j))
idx_v_i = list(set(idx_v_i))
idx_v_j = list(set(idx_v_j))
for count in range(up_left_count):
i_int = randint(0, len(idx_i) - 1)
j_int = randint(0, len(idx_j) - 1)
if m[i_int][j_int] != '←':
m[idx_i[i_int]][idx_j[j_int]] = '←'
for count_v in range(up_left_count):
i_v_int = randint(0, len(idx_v_i) - 1)
j_v_int = randint(0, len(idx_v_j) - 1)
if m[i_v_int][j_v_int] != '↑':
m[idx_v_i[i_v_int]][idx_v_j[j_v_int]] = '↑ '
for i in range(len(m)):
for j in range(len(m[0])):
if i % 2 == 0 and j % 2 != 0:
if m[i][j] == '?':
m[i][j] = '→'
for i in range(len(m)):
for j in range(len(m[0])):
if i % 2 != 0 and j % 2 == 0:
if m[i][j] != '↑ ':
m[i][j] = '↓ '
m[0][0] = "S"
m[-1][-1] = "D"
for i in range(len(m)):
for j in range(len(m[0])):
print(m[i][j], end=" ")
print()
path = []
return findPaths(m, path, 0,0)
if maze(5,6):
print('True')
else:
print('False')

Program doesn't work after making exe file by pyinstaller

I made a Python program using numpy, sympy, sys which worked well in IDE. Here is the code...
import numpy as np
from sympy import *
import sys
f = open("result.txt", 'w+')
for line in sys.stdin:
f.write(line)
f.close()
f = open("result.txt", 'r')
data = f.read().split("\n")
i = 0
while i < len(data):
data[i] = data[i].split(' ')
i += 1
print(data)
amount = int(data[0][0])
print(amount)
matrix = np.zeros((amount, amount))
i = 0
j = 0
while i < amount:
while j < amount:
matrix[i, j] = int(data[i + 1][j])
j += 1
j = 0
i += 1
i = 0
j = 0
counter = 0
formula = 1
while i < amount:
while j < amount:
if matrix[i, j] == 1:
x = symbols(str(i + 1))
y = symbols(str(j + 1))
if counter == 0:
formula = (~x | ~y)
counter += 1
else:
formula = formula & (~x | ~y)
j += 1
j = 0
i += 1
formula_to_string = pycode(simplify_logic(formula, form='dnf', force=True))
massive_to_parse = formula_to_string.split("or")
k = 1
i = 0
while i < len(massive_to_parse):
print("{", end='')
while k < amount + 1:
try:
massive_to_parse[i].index(str(k))
except ValueError:
print("V",k, sep='', end='')
finally:
k += 1
print("}-максимальное внутренне устойчивое множество")
k = 1
i += 1
Then I made an exe file using pyinstaller with this command...
pyinstaller main.py
but when i launch it, this errors appear.
How can I fix this problem? Because I need exe file for university to launch it from other program on C

Russian Peasant Multiplication Python using recursive-tail

I tried making this code and run it, but the result showed "None".
I've edited by adding another else in the loop function, then it actually produces a int result of '57' which is not exactly the answer.
def double(n):
return n*2
def halve(n):
return n//2
def mult(m,n):
def loop(m,n):
if n>1:
if n%2 != 0:
return m + loop(double(m),halve(n))
else:
return m #added another else
else:
return m
if n>0:
return loop(m,n)
else:
return 0
print(mult(57,86))

by simple recursion
def double(n):
return n * 2
def halve(n):
return n // 2
def mult(m, n, a = 0):
if n % 2 != 0:
a = a + m
m = double(m)
n = halve(n)
if n % 2 == 0:
m = double(m)
n = halve(n)
if n != 0:
return mult(m, n, a)
return a
print(mult(57, 86))
by nested function
def double(n):
return n * 2
def halve(n):
return n // 2
def mult(m, n):
def loop(m, n, a = 0):
if n % 2 != 0:
a = a + m
m = double(m)
n = halve(n)
if n % 2 == 0:
m = double(m)
n = halve(n)
if n != 0:
return loop(m, n, a)
return a
return loop(m, n)
print(mult(57, 86))

returning values in python

i have a code which looks like this
def monokode(b):
while f == 0:
if g[h]== b[i]:
i = i + 1
j = h - e
if j >= 100:
j = (e-h + len(g))*-1
elif j <= -100:
j = (e-h - len(g))*-1
if j < 10 and j >=0:
print 0,0,j,
elif j < 0:
j = j*-1
if j < 10:
print 1,0,j,
elif j >= 10 and j < 100:
print 1,j,
else:
print 1,j,
elif j >= 10 and j < 100:
print 0,j,
else:
print 0,j,
h = 0
if i >= len(b):
f = 1
else:
h=h+1
now, i want to make all the statements that print right now, return their value instead. but after some tries, i've realised that i don't know enough about the return statement to use it properly. how can i make the program return multiple values in a long line and then print them afterwards?

UPDATED ANSWER:
Okay as I understand the question you're wanting to make your function return multiple variables and then print them?
I agree with most of the other replies. Store the objects you want to print in a list then call
print ', '.join(list)
right before you return whatever values from the program:
like this:
def monokode(b):
printspool=[]
while f == 0:
if g[h]== b[i]:
i = i + 1
j = h - e
if j >= 100:
j = (e-h + len(g))*-1
elif j <= -100:
j = (e-h - len(g))*-1
if j < 10 and j >=0:
printspool.append([0,0,j])
elif j < 0:
j = j*-1
if j < 10:
printspool.append([1,0,j])
elif j >= 10 and j < 100:
printspool.append([1,j])
else:
printspool.append([1,j])
elif j >= 10 and j < 100:
printspool.append([0,j])
else:
printspool.append([0,j])
h = 0
if i >= len(b):
f = 1
else:
h=h+1
#Now here I'll print out everything contained in the printspooler list
for node in printspooler:
print ','.join(node)
#This is where you would
return Whatevervariable, Whatevervariable2, Whatevervariable3 etc...

Collect your values into a list instead, then return that list:
def yourfunction(your_arguments):
results = []
while f == 0:
if g[h]== b[i]:
i = i + 1
j = h - e
if j >= 100:
j = (e-h + len(g))*-1
elif j <= -100:
j = (e-h - len(g))*-1
if j < 10 and j >=0:
results.extend([0,0,j])
elif j < 0:
j = j*-1
if j < 10:
results.extend([1,0,j])
elif j >= 10 and j < 100:
results.extend([1,j])
else:
results.extend([1,j])
elif j >= 10 and j < 100:
results.extend([0,j])
else:
results.extend([0,j])
h = 0
if i >= len(b):
f = 1
else:
h=h+1
return results

You can use return and say many variable names...
return a, b, c
and what is returned is a tuple in the same order..
eg. return 1, 2, 3
will be (1, 2, 3)
and you can directly print call_fn() # if this returns those values

From what I understand, you can to store the values into a list:
def myfunc(…)
…
myList=[]
while f == 0:
if g[h]== b[i]:
i = i + 1
j = h - e
if j >= 100:
j = (e-h + len(g))*-1
elif j <= -100:
j = (e-h - len(g))*-1
if j < 10 and j >=0:
myList.extend([0,0,j])
elif j < 0:
j = j*-1
if j < 10:
myList.extend([1,0,j])
elif j >= 10 and j < 100: #this test
myList.extend([1,j])
else:
myList.extend([1,j])
elif j >= 10 and j < 100: #and this one
myList.extend([0,j])
else:
myList.extend([0,j])
h = 0
if i >= len(b):
f = 1
else:
h=h+1
return myList
and then print myFunc(…), or maybe something like
results = myFunc(…)
for r in results:
print r,
Edit: I've marked 2 tests that I think are unnecessary, since in the èlse part, you print the same thing