from sys import argv, exit
import re
if len(argv) < 2:
    print("mising command-line argument")
    exit(1)
pattern1 = re.compile(r'AGAT')
pattern2 = re.compile(r'AATG')
pattern3 = re.compile(r'TATC')
with open(argv[1], "r") as f:
    count = 0
    contents = f.read()
    print(contents)
    print(contents[0:4])
    i = 0
    j = i + 4
    while contents[i:j]: # will read contents until end of file
        span = contents[i:j] # initially set span to contents 1-4
        while contents[i+4:j+4] == span: # while the following 4 characters are equal to the characters in span
        #while span[i+4:j+4] == span[i:j]:
            count += 1 # increment count
            print("span " + span + "repeats " + str(count) + " times" )
        i += 1
        j += 1
    i += 1
    j += 1
#The bug as stated in your other
#similar post is that i and j are only
#incremented inside your inner loop on
#condition you find a match. So if no match,
#your outer loop keeps checking the same
#part of contents[i][j] over and over