You can use input:

# the first line contains integer
integer1 = int(input())

# the second line contains the space separated list of integers
int_lst = list(map(int, input().split()))

# third line contains another integer.
integer2 = int(input())

list of lists for 10 lines:

lst = [list(map(int, input().split())) for _ in range(10)]

The reason that you are getting the error is that readlines is consuming all your input on the first call. That means that the second time you call it, there's nothing there.

To make a 2D list of all the inputs, you have to work with the first call:

data = [line.rstrip().split() for line in sys.stdin.readlines()]

You may as well convert to integers up front:

data = [[int(x) for x in row] for row in data]

Now

arr = data[0]
A = set(data[2])
B = set(data[3])

You can redirect the stdin with < on command line. Let's say you have following input stored to file data.in:

line1
line2

And you have following code stored to test.py:

print(1, input())
print(2, input())

Then you can run the script with redirected stdin:

~$ python3 test.py < data.in
1 line1
2 line2

If you want to save the output to a file you can redirect stdout as well:

~$ python3 test.py < data.in > data.out