old_contents: #!/usr/bin/env python
  
  import argparse
  import sys
  from codonpdx.calc import calcScore
  from codonpdx.count import codonCount
  from codonpdx.insert import loadDB
  
  # create the top-level parser
  parser = argparse.ArgumentParser(prog='codonpdx',
                                   description='codonpdx command line util')
  parser.add_argument('--version', action='version', version='%(prog)s 1.0')
  subparsers = parser.add_subparsers(help='sub-command help')
  
  # create the parser for the "count" command
  parserCount = subparsers.add_parser('count', help='codon counter')
  parserCount.add_argument('-i', '--infile', nargs='?',
                           type=argparse.FileType('r'), default=sys.stdin,
                           help='a file path')
  parserCount.add_argument('-f', '--format', choices=['fasta', 'genbank'],
                           help='the file format')
  parserCount.add_argument('-p', '--pretty', action='store_true',
                           help='enable json pretty print')
  parserCount.set_defaults(func=codonCount)
  
  # create the parser for the "loadDB" command
  parserLoadDB = subparsers.add_parser('loadDB',
                                       help='stores codon count metadata')
  parserLoadDB.add_argument('-d', '--dbname', choices=['refseq', 'genbank'],
                            help='the dbname to store the count metadata')
  parserLoadDB.add_argument('-i', '--infile', nargs='?',
                            type=argparse.FileType('r'), default=sys.stdin,
                            help='a file path')
  parserLoadDB.set_defaults(func=loadDB)
  
  
  # create the parser for the "calcScore" command
  parserCalcScore = subparsers.add_parser(
      'calcScore',
      help='calculate the codon count scores'
  )
  parserCalcScore.add_argument('-d', '--dbname', choices=['refseq', 'genbank'],
                               help='the dbname to fetch the count metadata')
  parserCalcScore.add_argument('-v', '--virus', required=True,
                               help='the virus id to compare against')
  parserCalcScore.set_defaults(func=calcScore)
  
  args = parser.parse_args()
  args.func(args)
  
new_contents: #!/usr/bin/env python
  
  import argparse
  import sys
  from codonpdx.calc import calcScore
  from codonpdx.count import codonCount
  from codonpdx.insert import loadDB
  
  # create the top-level parser
  parser = argparse.ArgumentParser(prog='codonpdx',
                                   description='Codonpdx command line utility.')
  parser.add_argument('--version', action='version', version='%(prog)s 1.0')
  subparsers = parser.add_subparsers(help='Sub-command descriptions:')
  
  # create the parser for the "count" command
  parserCount = subparsers.add_parser('count', help='Count the codons of a file and produce JSON output containing the results.')
  parserCount.add_argument('-i', '--infile', nargs='?',
                           type=argparse.FileType('r'), default=sys.stdin,
                           help='A file containing sequence data.')
  parserCount.add_argument('-f', '--format', choices=['fasta', 'genbank'],
                           help='The file format.')
  parserCount.add_argument('-p', '--pretty', action='store_true',
                           help='Print the JSON in a pretty, more human-readable way.')
  parserCount.set_defaults(func=codonCount)
  
  # create the parser for the "loadDB" command
  parserLoadDB = subparsers.add_parser('insert',
                                       help='Insert organism codon count JSON information into the database.')
  parserLoadDB.add_argument('-d', '--dbname', choices=['refseq', 'genbank'],
                            help='The database table to store the count information in.')
  parserLoadDB.add_argument('-i', '--infile', nargs='?',
                            type=argparse.FileType('r'), default=sys.stdin,
                            help='The file to to read the JSON data from. Defaults to standard input.')
  parserLoadDB.set_defaults(func=loadDB)
  
  
  # create the parser for the "calcScore" command
  parserCalcScore = subparsers.add_parser(
      'calc',
      help='Compare an organism to all other organisms in a given sequence database.'
  )
  parserCalcScore.add_argument('-d', '--dbname', choices=['refseq', 'genbank'],
                               help='The sequence database to compare the organism to.')
  parserCalcScore.add_argument('-v', '--virus', required=True,
                               help='The accession.version number of the organism to compare. (Currently must be located in the sequence database to compare against.)')
  parserCalcScore.set_defaults(func=calcScore)
  
  args = parser.parse_args()
  args.func(args)
  
subject: Add some detail to the help messages given by the program.