from jcvi.apps.base import OptionParser # Initialize the parser parser = OptionParser(usage="usage: %prog [options] input_file output_file") # Add some options parser.add_option("-f", "--format", dest="format", default="csv", help="output format: csv (default), json, or xml") parser.add_option("-v", "--verbose", dest="verbose", action="store_true", help="enable verbose output") # Parse the arguments (options, args) = parser.parse_args() # Use the arguments in your script logic input_file = args[0] output_file = args[1] if options.format == "csv": # Write csv output elif options.format == "json": # Write json output elif options.format == "xml": # Write xml output if options.verbose: print("Verbose output enabled")In this example, the script expects two positional arguments, input_file and output_file, which are specified when running the script. The user can also specify two optional arguments, format and verbose, by adding the -f or -v flags respectively. OptionParser then parses these arguments and stores them in the options and args variables. These variables can be used in the script to modify its behavior, such as selecting a specific output format and enabling/disabling verbose output. Overall, OptionParser is a useful library for creating command-line interfaces for Python scripts, and is included in the jcvi package library for genome analysis tools.