Python can't parse command line arguments

Question

I'm trying to get the arguments by using getopt

import sys
import getopt
import time
from datetime import timedelta
start_time = time.monotonic()


filename = ''
startIndex = 1
debug = False
outputFile = 'output.csv'

try:
    opts, args = getopt.getopt(sys.argv[1:], "hc:o:", ["help","counter=", "output="])
except getopt.GetoptError as err:
        # print help information and exit:
        print(err)  # will print something like "option -a not recognized"
        sys.exit(2)
 
for opt, arg in opts:
   if opt == '-h':
      print ('help info')
      sys.exit()
   elif opt in ("-o", "--output"):
      outputfile = arg
   elif opt in ("-c", "--counter"):
      startIndex = arg

filename = sys.argv[1]

print(outputFile)
print(startIndex)
print(debug)
print(opts)
print(args)

Output:

 python pSRA.py rs.txt -o out.csv -c 3 
output.csv
1
False
[]
['rs.txt', '-o', 'out.csv', '-c', '3']

when printing the args they are all there, however opts is an empty list. What am I doing wrong?

Answer 1

From the docs:

Note: Unlike GNU getopt(), after a non-option argument, all further arguments are considered also non-options. This is similar to the way non-GNU Unix systems work.

rs.txt is a non-option argument, so everything after it is also considered a non-option argument.

If you want GNU-style behavior, you can use getopt.gnu_getopt(), or if you aren't particularly attached to getopt, you can use a different argument parser, like argparse.