docs: def addFASTACommandLineOptions(parser):
      """
      Add standard command-line options to an argparse parser.
  
      @param parser: An C{argparse.ArgumentParser} instance.
      """
  
      parser.add_argument(
          '--fastaFile', type=open, default=sys.stdin, metavar='FILENAME',
          help=('The name of the FASTA input file. Standard input will be read '
                'if no file name is given.'))
  
      parser.add_argument(
          '--readClass', default='DNARead', choices=readClassNameToClass,
          metavar='CLASSNAME',
          help=('If specified, give the type of the reads in the input. '
                'Possible choices: %s.' % ', '.join(readClassNameToClass)))
  
      # A mutually exclusive group for either --fasta, --fastq, or --fasta-ss
      group = parser.add_mutually_exclusive_group()
  
      group.add_argument(
          '--fasta', default=False, action='store_true',
          help=('If specified, input will be treated as FASTA. This is the '
                'default.'))
  
      group.add_argument(
          '--fastq', default=False, action='store_true',
          help='If specified, input will be treated as FASTQ.')
  
      group.add_argument(
          '--fasta-ss', dest='fasta_ss', default=False, action='store_true',
          help=('If specified, input will be treated as PDB FASTA '
                '(i.e., regular FASTA with each sequence followed by its '
                'structure).'))