Using getopt module to parse and define command line arguments in python

Question

[uxue33]

I'm beginning to learn how to use python to develop some tasks in the lab.

I have tried to use the getopt.getopt method to define the command line arguments but when I run the program gives an error, telling that output_file is not defined.

Here is my code:

  def main(argv):

       lista_file = ''
       fasta_file = ''
       output_file = ''

       try:
          opts, args = getopt.getopt(argv,"l:f:o:",["lista=","fasta=", "output="])
       except getopt.GetoptError:
          print 'test.py -l <lista> -f <fasta>'
          sys.exit(2)
       for opt, arg in opts:
          if opt in ("-l", "--lista"):
             lista_file = arg
          elif opt in ("-f", "--fasta"):
             fasta_file = arg
          elif opt in ("-o", "--output"):
             output_file = arg

          print 'Lista is:  "', lista_file
          print 'Fasta is "', fasta_file
          print 'Output is "', output_file

       return lista_file
       return fasta_file
       return output_file

    if __name__ == "__main__":
     main(sys.argv[1:])

Thanks in advanced,

Uxue

[James Ashmore]

The getopt module is deprecated, I'd suggest learning the new argparse module.

Answer 1

[Asaf]

This is not how you should use it. You better use argparse instead of getopt. I use a skeleton script, many of whom can be found online, e.g.

	#!python
	"""See main.__doc__"""
	import os
	import logging
	import glob
	import unittest
	import sys
	import click
	import click.testing
	module = sys.modules["__main__"].__file__
	log = logging.getLogger(module)
	def process(filename, output):
	"""Do something more useful that printing out the file name"""
	print(filename)
	@click.command()
	@click.argument("files", nargs=-1)
	@click.option(
	"--output",
	help="output directory where to write to",
	default=os.getenv("TEMP"),
	type=click.Path(),
	)
	@click.option("--verbose", "-v", help="increases verbosity", count=True)
	def main(files, output, verbose):
	"""This help line will show in the command line --help output"""
	logging.root.setLevel(max(3 - verbose, 0) * 10) # impact all loggers
	log.debug("log level: %s", log.getEffectiveLevel())
	log.debug("output: %s", output)
	# credit https://stackoverflow.com/questions/48604754
	all_files = []
	for argument in files:
	log.debug("processing argument %s ...", argument)
	# if our shell does not do filename globbing
	expanded = list(glob.glob(argument))
	if len(expanded) == 0 and "*" not in argument:
	raise (click.BadParameter("{}: file not found".format(argument)))
	all_files.extend(expanded)
	# Actual processing of the files.
	for filename in all_files:
	log.info("processing file %s ...", filename)
	process(filename, output)
	if __name__ == "__main__":
	logging.basicConfig(
	stream=sys.stderr,
	level=logging.DEBUG,
	format="%(name)s (%(levelname)s): %(message)s",
	)
	try:
	main()
	except KeyboardInterrupt:
	log.info("%s interrupted", module)
	finally:
	logging.shutdown()
	class BasicCommandLineTest(unittest.TestCase):
	"""Tests can be run with python -m unittest <script>"""
	def setUp(self):
	self.runner = click.testing.CliRunner()
	def test_offers_help_for_invalid_option(self):
	"""Shows usage when the option is not valid"""
	result = self.runner.invoke(main, ["--invalid"])
	self.assertEqual(result.exit_code, 2)
	self.assertRegex(result.output, r"Try.*--help")
	def test_shows_help(self):
	"""Makes sure the help is available."""
	result = self.runner.invoke(main, ["--help"])
	self.assertEqual(result.exit_code, 0)
	self.assertRegex(result.output, r"Usage: ")
	def test_one_v_for_info_level_logging(self):
	"""-v sets logging to info."""
	_ = self.runner.invoke(main, ["-v"])
	self.assertEqual(log.getEffectiveLevel(), logging.INFO)
	def test_two_v_for_info_level_logging(self):
	"""-vv sets logging to debug."""
	_ = self.runner.invoke(main, ["-vv"])
	self.assertEqual(log.getEffectiveLevel(), logging.DEBUG)

view raw bootstrap_cmdline.py hosted with ❤ by GitHub

. Whenever you start a new script copy this skeleton to a new file and start filling in the parameters and code. A good habit is not to have any parameter hard-coded in the code, if you're writing a line and need a parameter just add it to the parameters function and set a default value.

[uxue33]

Thank you very much for your help!

I will try to use this module from now on.