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

with open(argv[1],"r") as file, open(argv[2],"r") as csvfile:
    count = 0
    contents = file.read() #1. Read the sequence file into a string (you've got this).
    csvcontents = csv.reader(csvfile)
    #2. Open the csv file and get each sub string
    #("AGATC", "TCTG", etc) from the first row
    #into a list (you've essentially done this too).

    header = next(csvcontents)
    print("header prints")
    print(header)

    print("attempting to print rows of csvfile")
    for row in csvcontents:
        print(row)
    print("now header prints:")
    print(header)

    for item in header[1:]:
        beg = 0 # beginning index
        end = len(item) # item length
        seqrun = 0
        longest = 0
        while beg + end <= len(contents):
            seqrun = 0
            while contents[beg: beg + end] == item: # the first len(item) needs to be removed
                seqrun += 1
                beg += len(item)
                if seqrun > longest:
                    longest = seqrun
            beg += 1
            end += 1
        print(item + " repeats " + str(longest) + "times") # why is it longest?