text: import argparse
  import pandas as pd
  import numpy as np
  import os,sys, re
  sys.path.append(os.getcwd())
  from funtaxacount import merge_orf_and_funtax, get_function_counts
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser(description='Generate function counts')
      parser.add_argument( 'orf', nargs='?',
                           type=argparse.FileType('r'))
      parser.add_argument( 'funtax', nargs='?',
                           type=argparse.FileType('r'))
      parser.add_argument( 'read_counts', nargs='?',
                           type=argparse.FileType('r'))
  
      parser.add_argument( '--function', choices=['ec','KO', 'COG'], default='ec') 
      parser.add_argument( '--out', nargs='?',
                          type=argparse.FileType('w'), default=sys.stdout)
      args = parser.parse_args()
  
      function_counts = get_function_counts( args.function, args.orf.name, args.funtax.name, args.read_counts )
      function_counts.to_csv(args.out, sep='\t')
          
      
  