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 file:

    contents = file.read()
    i = 0
    j = 4
    while contents[i:j]:
            #this works.... save it... prints one string of 4 per line
        print(contents[i:j])
        i += 4
        #j += 4

    while contents[i:j]:
        if contents[i:j] == contents[i+4:j+4]:
            index = 1
            count = 1
            while contents[i:j] == contents[i+4*index:j+4*index]:
                i += 1
                j += 1
                count += 1
                index += 1
            print(str(contents[i:j]) + " count is: " + count)

    matchcount = 0
    i = 0
    j = 4
    while contents[i:j]:
        pattern = contents[i:j] #pattern = re.compile(pattern?)
        if pattern == contents[i+4:j+4]:
            #matches = pattern.finditer(contents)
            #matches = pattern.finditer(f'contents')
            mcount = 1
            for match in matches:
                #print(match)
                mcount += 1

        i += 1
        j += 1


    print("printing count, the number of times that pattern1 appears in the file, should return 5")
    print(mcount)
    print("mind you, these are not consecutive matches")