old_contents: #!/usr/bin/env python
  
  import argparse
  
  
  def parse_command_line(args=None):
      """
      The options
      for both the serotyper, and virulence finder.
      The returned object is used by both, but the options do not
      necessarily apply to both.
      """
  
      def check_percentage(value):
          ivalue = int(value)
          if ivalue <= 0 or ivalue > 100:
              raise argparse.ArgumentTypeError("%s is an invalid positive int percentage value" % value)
          return ivalue
  
      parser = argparse.ArgumentParser()
      parser.add_argument(
          "-i",
          "--input",
          help="Location of new file(s). Can be a single file or \
              a directory",
          required=True
      )
  
      parser.add_argument(
          "-d",
          "--percentIdentity",
          type=check_percentage,
          help="Percentage of identity wanted to use against the\
                    database. From 0 to 100, default is 90%%.",
          default=90
      )
  
      parser.add_argument(
          "-l",
          "--percentLength",
          type=check_percentage,
          help="Percentage of length wanted to use against the \
                    database. From 0 to 100, default is 50%%.",
          default=50
      )
  
      parser.add_argument(
          "--verify",
          action="store_true",
          help="Enable E. Coli. verification"
      )
  
      parser.add_argument(
          "-s",
          "--species",
          action="store_true",
          help="Enable non-ecoli species identification"
      )
      
      parser.add_argument(
          '-v',
          '--verbose',
          action='store_true',
          help='Enable detailed output'
      )
  
      parser.add_argument(
          "-o",
          "--output",
          help="Directory location of output files."
      )
  
      if args is None:
          return parser.parse_args()
      return parser.parse_args(args)
  
new_contents: #!/usr/bin/env python
  
  import argparse
  
  
  def parse_command_line(args=None):
      """
      The options
      for both the serotyper, and virulence finder.
      The returned object is used by both, but the options do not
      necessarily apply to both.
      """
  
      def check_percentage(value):
          ivalue = int(value)
          if ivalue <= 0 or ivalue > 100:
              raise argparse.ArgumentTypeError("%s is an invalid positive int percentage value" % value)
          return ivalue
  
      parser = argparse.ArgumentParser()
      parser.add_argument(
          "-i",
          "--input",
          help="Location of new file(s). Can be a single file or \
              a directory",
          required=True
      )
  
      parser.add_argument(
          "-d",
          "--percentIdentity",
          type=check_percentage,
          help="Percentage of identity wanted to use against the\
                    database. From 0 to 100, default is 90%%.",
          default=90
      )
  
      parser.add_argument(
          "-l",
          "--percentLength",
          type=check_percentage,
          help="Percentage of length wanted to use against the \
                    database. From 0 to 100, default is 50%%.",
          default=50
      )
  
      parser.add_argument(
          "--verify",
          action="store_true",
          help="Enable E. Coli. verification"
      )
  
      parser.add_argument(
          "-s",
          "--species",
          action="store_true",
          help="Enable species identification when non-ecoli genome is found\n\
              Note: refseq downloading is required when running this option for the first time."
      )
      
      parser.add_argument(
          '-v',
          '--verbose',
          action='store_true',
          help='Enable detailed output'
      )
  
      parser.add_argument(
          "-o",
          "--output",
          help="Directory location of output files."
      )
  
      if args is None:
          return parser.parse_args()
      return parser.parse_args(args)
  
subject: Add more informative description of --species argument