from sys import argv, exit
import csv
import re
if len(argv) < 3:
    print("mising command-line argument")
    exit(1)

#pattern1 = re.compile(r'AGAT')
#pattern2 = re.compile(r'AATG')
#pattern3 = re.compile(r'TATC')
# pattern = re.compile(r'contents[i:j]')

with open(argv[1],"r") as file:
    count = 0
    contents = file.read()

    i = 0
    j = 4
    while contents[i:j]:
        span = contents[i:j]
        repcount = 1
        while contents[i+4:j+4] == span:
            repcount += 1
            i += 4
            j += 4
        #if repcount != 0:
        if repcount > 1:
            print("span " + span + " repeats " + str(repcount) + " times")
            i += 4
            j += 4
        else:
            i += 4
            j += 4


        #index = 0    ### these lines won't recognize header, because it's declared in the next open statement
        #for headervalue in header: # for each value in the header
            #index += 1  # keep track of which index in the line you are looking at
            #if headervalue == span:  # if the value in the header matches the span that is looking to be matched
                #data = [row for row in contents] # look at each row of the
                #if int(data[index]) == repcount:
                    #print("possible match is named " + data[0])

with open(argv[2],"r") as csvfile:
    csvcontents = csv.reader(csvfile)
    header = next(csvcontents) # look up what next is doing again
    print("seeing what the next() function does by assigning it to header")
    print("printing header")
    print(header) ## assign header into a list

    data = [row for row in csvcontents]
    print("printing data[0]")

        # this line causes the program to crash, saying
        # valueError: invalid literal for int() with base 10: 'Neville'

    print(data[0]) # why don't lit let me print the name stored at data[0]?
    print("printing 1 line at a time")
    i = 0
    while i < len(data):
        print(data[i])
        i += 1
    print("print(data[15][2]) prints: ")
    print(int(data[15][2]))

    print("print(data[15][1]) prints: ")
    print(int(data[15][1]))

    print("print(data[15][0]) prints: ")


    print("header[1] prints: ")
    print(header[1])

    #print("printing everything in the csv file: ")
    #print(data)