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, open(argv[2],"r") as csvfile:


    count = 0
    contents = file.read()
    csvcontents = csv.reader(csvfile)

    header = next(csvcontents)
    print("every item of header: ")
    for string in header:
        print(string, end = " ,")
    for string in header:
        startindex = 0
        endindex = len(string)
        scount = 0
        longest = 0
        while contents[startindex:endindex]:
            span = contents[startindex:endindex]
            while contents[startindex + endindex: endindex + endindex ] == span:
            #while span = string:
                scount += 1
                startindex += endindex
                endindex += endindex
            if scount > 1:
                print("span " + span + " repeats " + str(scount) + " times")
                startindex += 1
                endindex += 1
            else:
                startindex += 1
                endindex += 1
            if contents[startindex + endindex: endindex + endindex] == span:
                scount += 1
                startindex += endindex
                endindex += endindex


    #i = 0
#    j = 4
 #   while contents[i:j]:
  #      span = contents[i:j]
   #     repcount = 0
    #    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
  #          i += 1
   #         j += 1
    #    else:
            #i += 4
            #j += 4
#            i += 1
 #           j += 1

#with open(argv[2]) as csvfile:
    #csvcontents = csvfile.read()