This function sets up a command-line option parser and then calls match_and_print
    to do all of the real work.
2032
def main(argv):
    
    import argparse
    import codecs
    # have to be ready to deal with utf-8 names
    out = codecs.getwriter('utf-8')(sys.stdout)

    description = 'Uses Open Tree of Life web services to find information for each OTT ID.'
    parser = argparse.ArgumentParser(prog='ot-taxon-info', description=description)
    parser.add_argument('ids', nargs='+', type=int, help='OTT IDs')
    parser.add_argument('--include-lineage', action='store_true', default=False, required=False,
                        help='list the IDs of the ancestors as well.')
    # uncomment when https://github.com/OpenTreeOfLife/taxomachine/issues/89 is fixed @TEMP
    # parser.add_argument('--list-tips', action='store_true', default=False, required=False,
    #                    help='list the tips in the subtree rooted by this taxon.')
    args = parser.parse_args(argv)
    id_list = args.ids
    list_tips = False  # args.list_tips once https://github.com/OpenTreeOfLife/taxomachine/issues/89 is fixed @TEMP
    fetch_and_write_taxon_info(id_list, args.include_lineage, list_tips, out)
811453
def execute(self):
        
        #Initialize the option parser
        parser = LaxOptionParser(
            usage="%prog subcommand [options] [args]",
            option_list=BaseCommand.option_list #This will define what is allowed input to the parser (ie --settings=)
        )

        #Parse the options
        options, args = parser.parse_args(self.argv)
        #Handle --settings and --pythonpath properly
        options = handle_default_options(options)

        try:
            #Get the name of the subcommand
            subcommand = self.argv[1]
        except IndexError:
            #If the subcommand name cannot be found, set it to help
            subcommand = 'help'

        #If the subcommand is help, print the usage of the parser, and available command names
        if subcommand == 'help':
            if len(args) <= 2:
                parser.print_help()
                sys.stdout.write(self.help_text + '\n')
        else:
            #Otherwise, run the given command
            self.fetch_command(subcommand).run_from_argv(self.argv)
928736
def execute(self):
        
        # Preprocess options to extract --settings and --pythonpath.
        # These options could affect the commands that are available, so they
        # must be processed early.
        parser = NewOptionParser(prog=self.prog_name,
                             usage=self.usage_info,
#                             version=self.get_version(),
                             formatter = NewFormatter(),
                             add_help_option = False,
                             option_list=self.option_list)
        
        if not self.global_options:
            global_options, args = parser.parse_args(self.argv)
            handle_default_options(global_options)
            args = args[1:]
        else:
            global_options = self.global_options
            args = self.argv
    
        def print_help(global_options):
            parser.print_help()
            sys.stderr.write(self.print_help_info(global_options) + '\n')
            sys.exit(0)
            
        if len(args) == 0:
            if global_options.version:
                print(self.get_version())
                sys.exit(1)
            else:
                print_help(global_options)
                sys.ext(1)
    
        try:
            subcommand = args[0]
        except IndexError:
            subcommand = 'help' # Display help if no arguments were given.
    
        if subcommand == 'help':
            if len(args) > 1:
                command = self.fetch_command(global_options, args[1])
                if issubclass(command, CommandManager):
                    cmd = command(['help'], None, '%s %s' % (self.prog_name, args[1]), global_options=global_options)
                    cmd.execute()
                else:
                    command().print_help(self.prog_name, args[1])
                sys.exit(1)
            else:
                print_help(global_options)
        if global_options.help:
            print_help(global_options)
        else:
            command = self.fetch_command(global_options, subcommand)
            if issubclass(command, CommandManager):
                cmd = command(args[1:], None, '%s %s' % (self.prog_name, subcommand), global_options=global_options)
                cmd.execute()
            else:
                cmd = command()
                cmd.run_from_argv(self.prog_name, subcommand, global_options, args[1:])
597631
def parse_options(args=None, config=True, rootdir=CURDIR, **overrides):  # noqa
    
    args = args or []

    # Parse args from command string
    options = PARSER.parse_args(args)
    options.file_params = dict()
    options.linters_params = dict()

    # Compile options from ini
    if config:
        cfg = get_config(str(options.options), rootdir=rootdir)
        for opt, val in cfg.default.items():
            LOGGER.info('Find option %s (%s)', opt, val)
            passed_value = getattr(options, opt, _Default())
            if isinstance(passed_value, _Default):
                if opt == 'paths':
                    val = val.split()
                if opt == 'skip':
                    val = fix_pathname_sep(val)
                setattr(options, opt, _Default(val))

        # Parse file related options
        for name, opts in cfg.sections.items():

            if name == cfg.default_section:
                continue

            if name.startswith('pylama'):
                name = name[7:]

            if name in LINTERS:
                options.linters_params[name] = dict(opts)
                continue

            mask = re.compile(fnmatch.translate(fix_pathname_sep(name)))
            options.file_params[mask] = dict(opts)

    # Override options
    _override_options(options, **overrides)

    # Postprocess options
    for name in options.__dict__:
        value = getattr(options, name)
        if isinstance(value, _Default):
            setattr(options, name, process_value(name, value.value))

    if options.concurrent and 'pylint' in options.linters:
        LOGGER.warning('Can\'t parse code asynchronously with pylint enabled.')
        options.concurrent = False

    return options
291090
def main(argv=None):
    
    # Get command line arguments, validate them, and normalize them
    opts = cmdparse.parse_args(argv)
    assert validate_opts.validate(opts)
    opts = normalize_opts.normalize(opts)

    if opts.verbose:
        # Update client: print input and output directories
        messages.print_input_output(opts)

    file_paths = fileparse.get_file_list(opts)
    assert validate_files.validate(file_paths, opts)

    if opts.verbose and opts.is_dir:
        # Update client: print files that will be parsed
        messages.print_files(opts, file_paths)

    # For now, only using default GitHub Markdown for parsing
    # Collect tag/anchor combinations
    collector = make_github_markdown_collector(opts)
    anchors, duplicate_tags = collector.collect(file_paths)
    assert validate_anchors.validate(anchors, duplicate_tags, opts)

    # Write files using previously found AnchorHub tags and generated anchors
    writer = make_github_markdown_writer(opts)
    counter = writer.write(file_paths, anchors, opts)

    if opts.verbose:
        if opts.is_dir:
            # Update client: print files that had modifications
            messages.print_modified_files(opts, anchors)
        # Print summary statistics
        messages.print_summary_stats(counter)
1032864
def main(print_cfg):
    """"""
    parser = argparse.ArgumentParser(description="mvmany.py -- MVtest helper script.", epilog="""
mvmany.py should be run with all arguments you would pass to mvtest.py, except
for those which are specific to a single node's settings (such as chromosome and
BP range). It will then generate a number of scripts which can be run
simultaneously on a cluster. Please be aware that this script does not attempt
to adjust walltimes according to size, and that the user should choose a
walltime that is long enough to allow the largest run to complete.
    """)
    parser.add_argument("-v", action="store_true", help="Print version number")

    parser.add_argument("--mvpath", type=str, default="mvtest.py", help="The path to mvtest.py if it's not found in PATH")
    parser.add_argument("--logpath", type=str, default="log", help="Where to write the logs to")
    parser.add_argument("--res-path", type=str, default="result", help="Where to write the results to")
    parser.add_argument("--script-path", type=str, default="scripts", help="Where to write the various scripts to")
    parser.add_argument("--template", type=argparse.FileType('r'), help="File containing cluster related information that will be written as header to the various files")
    parser.add_argument("--snps-per-job", type=float, default=1.0, help="Allow the user to .")
    parser.add_argument("--mem", type=str, default="2G", help="Memory required during runs")
    parser.add_argument("--walltime", type=str, default="3:00:00", help="Walltime to use")

    # Most of these will just be passed on directly to the various MVTest scripts.
    parser.add_argument("--exclude", type=str, help="Comma-delimited list of rsids to be excluded")
    parser.add_argument("--keep", type=str, help="Comma-delimited list of individuals to be analyzed")
    parser.add_argument("--remove", type=str, help="Comma-delimited list of individuals to be removed from analysis")

    parser.add_argument("--file", type=str, help="Prefix for .ped and .map files")
    parser.add_argument("--ped", type=argparse.FileType('r'), help="PLINK compatible .ped file")
    parser.add_argument("--map", type=argparse.FileType('r'), help="PLINK compatible .map file")
    parser.add_argument("--map3", action='store_true', help="MAP file has only 3 columns")
    parser.add_argument("--no-sex", action='store_true', help="Pedigree file doesn't have column 5 (sex)")
    parser.add_argument("--no-parents", action="store_true", help="Pedigree file doesn't have columns 3 and 4 (parents)")
    parser.add_argument("--no-fid", action="store_true", help="Pedigree file doesn't have column 1 (family ID)")
    parser.add_argument("--no-pheno", action="store_true", help="Pedigree file doesn't have column 6 (phenotype")
    parser.add_argument("--liability", action="store_true", help="Pedigree file has column 7 (liability)")

    parser.add_argument("--bfile", type=str, help="Prefix for .bed, .bim and .fam files")
    parser.add_argument("--bed", type=argparse.FileType('r'), help="Binary Ped file (.bed)")
    parser.add_argument("--bim", type=argparse.FileType('r'), help="Binary ped marker file (.bim)")
    parser.add_argument("--fam", type=argparse.FileType('r'), help="Binary ped family file (.fam)")

    parser.add_argument("--tfile", type=str, help="Prefix for .tped and .tfam files")
    parser.add_argument("--tped", type=argparse.FileType('r'), help="Transposed Pedigree file (.tped)")
    parser.add_argument("--tfam", type=argparse.FileType('r'), help="Transposed pedigre Family file (.tfam)")
    parser.add_argument("--compressed", action="store_true", help="Ped/TPed compressed with gzip (named .ped.tgz or .tped.tgz)")


    parser.add_argument("--impute", type=argparse.FileType('r'), help="File containing list of impute output for analysis")
    parser.add_argument("--impute-fam", type=argparse.FileType('r'), help="File containing family details for impute data")
    parser.add_argument("--impute-count", type=int, help="Number of impute files to process on a single node")
    parser.add_argument("--impute-uncompressed", action="store_true", help="Indicate that the impute input is not gzipped, but plain text")
    parser.add_argument("--impute-encoding", type=str, choices=['additive', 'dominant', 'recessive', 'genotype'], help='Genetic model to be used')
    parser.add_argument("--impute-info-ext", type=str, help="Portion of filename denotes info filename")
    parser.add_argument("--impute-gen-ext", type=str, help="Portion of filename that denotes gen file")
    parser.add_argument("--impute-info-thresh", type=float, help="Threshold for filtering imputed SNPs with poor 'info' values")
    parser.add_argument("--impute-files-per-job", type=int, help="How many gen files to run per job")

    parser.add_argument("--mach", type=argparse.FileType('r'), help="File containing list of MACH output for analysis")
    parser.add_argument("--mach-uncompressed", action="store_true", help="Indicate that the mach input is not gzipped")
    parser.add_argument("--mach-info-ext", type=str, help="Portion of filename denotes info filenames")
    parser.add_argument("--mach-dose-ext", type=str, help="Portion of filename that denotes dose files")
    parser.add_argument("--mach-min-rsquared", type=float, help="Filter out loci with RSquared < this value")
    parser.add_argument("--mach-files-per-job", type=int, help="How many dosage files to run per job")
    parser.add_argument("--mach-chunk-size", type=int, help="How many loci to keep in memory at once")
    parser.add_argument("--mach-count", type=int, help="Number of mach files to process for each job")

    parser.add_argument("--pheno", type=argparse.FileType('r'), help="File containing phenotypes")
    parser.add_argument("--sample-pheno", type=argparse.FileType('r'), help="(Mach) Sample file containing phenotypes")
    parser.add_argument("--mphenos", type=str, help="Column number(s) for phenotype to be analyzed if number of columns > 1")
    parser.add_argument("--pheno-names", type=str, help="Name for phenotype(s) to be analyzed (must be in --pheno file)")
    parser.add_argument("--all-pheno", action="store_true", help="Analyze all columns from the phenotype file")

    parser.add_argument("--covar", type=argparse.FileType('r'), help="File containing covariates")
    parser.add_argument("--sample-covar", type=argparse.FileType('r'), help="(Mach) Sample file containing covariates")
    parser.add_argument("--covar-numbers", type=str, help="Comma-separated list of covariate indices")
    parser.add_argument("--covar-names", type=str, help="Comma-separated list of covariate names")
    parser.add_argument("--sex", action='store_true', help="Use sex from the pedigree file as a covariate")
    parser.add_argument("--missing-phenotype", type=float, help="Encoding for missing phenotypes")

    parser.add_argument("--maf", type=float, help="Minimum MAF allowed for analysis")
    parser.add_argument("--max-maf", type=float, help="MAX MAF allowed for analysis")
    parser.add_argument("--geno", type=float, help="MAX per-SNP missing for analysis")
    parser.add_argument("--mind", type=float, help="MAX per-person missing")

    parser.set_defaults(all_pheno=False, sex=False)
    args = parser.parse_args()

    # Report version, if requested, and exit
    if args.v:
        print >> sys.stderr, "%s: %s" % (os.path.basename(__file__), __version__)
        sys.exit(0)
    mkdir(args.script_path)
    mkdir(args.res_path)
    mkdir(args.logpath)

    if args.mach:
        args.mach = args.mach.name
    if args.impute:
        args.impute = args.impute.name
    if args.impute_fam:
        args.impute_fam = args.impute_fam.name
    if args.covar:
        args.covar = args.covar.name
    if args.pheno:
        args.pheno = args.pheno.name

    general_arguments = []
    for flag in ("exclude,keep,remove,file,ped,map,map3,no-sex,no-parents,no-fid,no-pheno,liability," + \
                        "bfile,bed,bim,fam,tfile,tped,tfam,compressed," + \
                        "impute,impute-fam,impute-uncompresed,impute-encoding,impute-info-ext,impute-gen-ext,impute-info-thresh," +\
                        "mach,mach-uncompressed,mach-info-ext,mach-dose-ext,mach-min-rsquared,mach-chunk-size," +\
                        "pheno,sample-pheno,pheno-names,mphenos,all-pheno," + \
                        "covar,sample-covar,covar-numbers,covar-names,sex,missing-phenotype,maf,max-maf,gen,mind").split(","):
        check_and_append(args, flag, general_arguments)

    args.template = get_template_file(args)
    job_list = None
    map_file = None
    impute_file_list = None
    if args.file:
        map_file = "%s.map" % (args.file)
    elif args.map:
        map_file = args.map
    elif args.bfile:
        map_file = "%s.bim" % (args.bfile)
    elif args.bim:
        map_file = args.bim
    elif args.tfile:
        map_file = "%s.tped"
    elif args.tped:
        map_file = args.tped
    elif args.impute:
        impute_file_list = args.impute

    max_snp_count = args.snps_per_job

    if map_file is not None:
        job_list = split_chrom_jobs(args, map_file)

    elif args.impute is not None:
        job_list = split_impute_jobs(args, args.impute)

    elif args.mach is not None:
        job_list = split_mach_jobs(args, args.mach)

    if job_list is None or len(job_list) == 0:
        parser.print_usage(sys.stderr)
        print >> sys.stderr, "\nThere were not jobs created. Did you specify the necessary data?"
    else:
        generate_jobs(args, job_list, " ".join(general_arguments))
    sys.exit(0)
486453
def main(raw_args=None):
    """"""
    parser = argparse.ArgumentParser(
        description="poor man's integration testing")
    parser.add_argument(
        'cmds', metavar='cmd', default=['test'], nargs='*',
        help='Run command(s) defined in the configuration file. Each command '
             'is run on each package before proceeding with the next command. '
             '(default: "test")')
    parser.add_argument(
        '-c', '--config', dest='file', type=argparse.FileType('r'),
        default='toll.ini',
        help='ini-style file to read the configuration from')
    parser.add_argument(
        '--start-at', dest='start_at', type=str, default='',
        help='Skip over the packages in the config file listed before this'
             ' one. (It does a substring match to find the first package.)')

    args = parser.parse_args(raw_args)
    config_file = config.parsed_file(args.file)
    commands = config.commands(config_file, args.cmds)
    packages = config.packages(config_file)
    runner = Runner(commands, packages, start_at=args.start_at)
    return runner()
553309
def main():
    
    args = parser.parse_args()
    try:
        function = args.func
    except AttributeError:
        parser.print_usage()
        parser.exit(1)
    function(vars(args))
248271
def main():
    
    # Define Parser object and add to jobTree
    parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawTextHelpFormatter)

    # Generate subparsers
    subparsers = parser.add_subparsers(dest='command')
    subparsers.add_parser('generate-config',
                          help='Generates an editable config in the current working directory.')
    subparsers.add_parser('generate-manifest',
                          help='Generates an editable manifest in the current working directory.')
    subparsers.add_parser('generate',
                          help='Generates a config and manifest in the current working directory.')

    # Run subparser
    parser_run = subparsers.add_parser('run', help='Runs the GATK germline pipeline')
    parser_run.add_argument('--config',
                            required=True,
                            type=str,
                            help='Path to the (filled in) config file, generated with '
                                 '"generate-config".')
    parser_run.add_argument('--manifest',
                            type=str,
                            help='Path to the (filled in) manifest file, generated with '
                                 '"generate-manifest".\nDefault value: "%(default)s".')
    parser_run.add_argument('--sample',
                            default=None,
                            nargs=2,
                            type=str,
                            help='Input sample identifier and BAM file URL or local path')
    parser_run.add_argument('--output-dir',
                            default=None,
                            help='Path/URL to output directory')
    parser_run.add_argument('-s', '--suffix',
                            default=None,
                            help='Additional suffix to add to the names of the output files')
    parser_run.add_argument('--preprocess-only',
                            action='store_true',
                            help='Only runs preprocessing steps')

    Job.Runner.addToilOptions(parser_run)
    options = parser.parse_args()

    cwd = os.getcwd()
    if options.command == 'generate-config' or options.command == 'generate':
        generate_file(os.path.join(cwd, 'config-toil-germline.yaml'), generate_config)
    if options.command == 'generate-manifest' or options.command == 'generate':
        generate_file(os.path.join(cwd, 'manifest-toil-germline.tsv'), generate_manifest)
    elif options.command == 'run':
        # Program checks
        for program in ['curl', 'docker']:
            require(next(which(program)),
                    program + ' must be installed on every node.'.format(program))

        require(os.path.exists(options.config), '{} not found. Please run "generate-config"'.format(options.config))

        # Read sample manifest
        samples = []
        if options.manifest:
            samples.extend(parse_manifest(options.manifest))

        # Add BAM sample from command line
        if options.sample:
            uuid, url = options.sample
            # samples tuple: (uuid, url, paired_url, rg_line)
            # BAM samples should not have as paired URL or read group line
            samples.append(GermlineSample(uuid, url, None, None))

        require(len(samples) > 0,
                'No samples were detected in the manifest or on the command line')

        # Parse inputs
        inputs = {x.replace('-', '_'): y for x, y in
                  yaml.load(open(options.config).read()).iteritems()}

        required_fields = {'genome_fasta',
                           'output_dir',
                           'run_bwa',
                           'sorted',
                           'snp_filter_annotations',
                           'indel_filter_annotations',
                           'preprocess',
                           'preprocess_only',
                           'run_vqsr',
                           'joint_genotype',
                           'run_oncotator',
                           'cores',
                           'file_size',
                           'xmx',
                           'suffix'}

        input_fields = set(inputs.keys())
        require(input_fields > required_fields,
                'Missing config parameters:\n{}'.format(', '.join(required_fields - input_fields)))

        if inputs['output_dir'] is None:
            inputs['output_dir'] = options.output_dir

        require(inputs['output_dir'] is not None,
                'Missing output directory PATH/URL')

        if inputs['suffix'] is None:
            inputs['suffix'] = options.suffix if options.suffix else ''

        if inputs['preprocess_only'] is None:
            inputs['preprocess_only'] = options.preprocess_only

        if inputs['run_vqsr']:
            # Check that essential VQSR parameters are present
            vqsr_fields = {'g1k_snp', 'mills', 'dbsnp', 'hapmap', 'omni'}
            require(input_fields > vqsr_fields,
                    'Missing parameters for VQSR:\n{}'.format(', '.join(vqsr_fields - input_fields)))

        # Check that hard filtering parameters are present. If only running preprocessing steps, then we do
        # not need filtering information.
        elif not inputs['preprocess_only']:
            hard_filter_fields = {'snp_filter_name', 'snp_filter_expression',
                                  'indel_filter_name', 'indel_filter_expression'}
            require(input_fields > hard_filter_fields,
                    'Missing parameters for hard filtering:\n{}'.format(', '.join(hard_filter_fields - input_fields)))

            # Check for falsey hard filtering parameters
            for hard_filter_field in hard_filter_fields:
                require(inputs[hard_filter_field], 'Missing %s value for hard filtering, '
                                                   'got %s.' % (hard_filter_field, inputs[hard_filter_field]))

        # Set resource parameters
        inputs['xmx'] = human2bytes(inputs['xmx'])
        inputs['file_size'] = human2bytes(inputs['file_size'])
        inputs['cores'] = int(inputs['cores'])

        inputs['annotations'] = set(inputs['snp_filter_annotations'] + inputs['indel_filter_annotations'])

        # HaplotypeCaller test data for testing
        inputs['hc_output'] = inputs.get('hc_output', None)

        # It is a toil-scripts convention to store input parameters in a Namespace object
        config = argparse.Namespace(**inputs)

        root = Job.wrapJobFn(run_gatk_germline_pipeline, samples, config)
        Job.Runner.startToil(root, options)
555147
def create_parser(self):
        
        return OptionParser(prog=self.prog_name,
                            usage=self.usage(),
                            version='%%prog %s' % self.get_version(),
                            option_list=self.option_list)
61600
def main():
    
    parser = argparse.ArgumentParser()
    sub_parser = parser.add_subparsers()

    lint_parser = sub_parser.add_parser('lint')
    lint_parser.set_defaults(func=lint)

    unit_test_parser = sub_parser.add_parser('unit-test')
    unit_test_parser.set_defaults(func=unit_test)

    test_suite_parser = sub_parser.add_parser('test-suite')
    test_suite_parser.set_defaults(func=test_suite)

    args, extra_args = parser.parse_known_args()

    if extra_args:
        args.func(extra_args)
    else:
        args.func()
660103
def main():
    
    import argparse

    parser = argparse.ArgumentParser(
        description="ftfy (fixes text for you), version %s" % __version__
    )
    parser.add_argument('filename', default='-', nargs='?',
                        help='The file whose Unicode is to be fixed. Defaults '
                             'to -, meaning standard input.')
    parser.add_argument('-o', '--output', type=str, default='-',
                        help='The file to output to. Defaults to -, meaning '
                             'standard output.')
    parser.add_argument('-g', '--guess', action='store_true',
                        help="Ask ftfy to guess the encoding of your input. "
                             "This is risky. Overrides -e.")
    parser.add_argument('-e', '--encoding', type=str, default='utf-8',
                        help='The encoding of the input. Defaults to UTF-8.')
    parser.add_argument('-n', '--normalization', type=str, default='NFC',
                        help='The normalization of Unicode to apply. '
                             'Defaults to NFC. Can be "none".')
    parser.add_argument('--preserve-entities', action='store_true',
                        help="Leave HTML entities as they are. The default "
                             "is to decode them, as long as no HTML tags "
                             "have appeared in the file.")

    args = parser.parse_args()

    encoding = args.encoding
    if args.guess:
        encoding = None

    if args.filename == '-':
        # Get a standard input stream made of bytes, so we can decode it as
        # whatever encoding is necessary.
        file = sys.stdin.buffer
    else:
        file = open(args.filename, 'rb')

    if args.output == '-':
        outfile = sys.stdout
    else:
        if os.path.realpath(args.output) == os.path.realpath(args.filename):
            sys.stderr.write(SAME_FILE_ERROR_TEXT)
            sys.exit(1)
        outfile = open(args.output, 'w', encoding='utf-8')

    normalization = args.normalization
    if normalization.lower() == 'none':
        normalization = None

    if args.preserve_entities:
        fix_entities = False
    else:
        fix_entities = 'auto'

    try:
        for line in fix_file(file, encoding=encoding,
                             fix_entities=fix_entities,
                             normalization=normalization):
            try:
                outfile.write(line)
            except UnicodeEncodeError:
                if sys.platform == 'win32':
                    sys.stderr.write(ENCODE_ERROR_TEXT_WINDOWS)
                else:
                    sys.stderr.write(ENCODE_ERROR_TEXT_UNIX)
                sys.exit(1)
    except UnicodeDecodeError as err:
        sys.stderr.write(DECODE_ERROR_TEXT % (encoding, err))
        sys.exit(1)
155223
def create_parser(self, prog_name, subcommand):
        
        if not self.use_argparse:
            self.__class__.option_list = TestCommand.option_list + self.custom_options
        parser = super(Command, self).create_parser(prog_name, subcommand)
        return parser
1098790
def build_arg_parser2():
    
    usage_str = "Smatch calculator -- arguments"
    parser = optparse.OptionParser(usage=usage_str)
    parser.add_option("-f", "--files", nargs=2, dest="f", type="string",
                      help='Two files containing AMR pairs. AMRs in each file are ' \
                           'separated by a single blank line. This option is required.')
    parser.add_option("-r", "--restart", dest="r", type="int", help='Restart number (Default: 4)')
    parser.add_option('--significant', dest="significant", type="int", default=2,
                      help='significant digits to output (default: 2)')
    parser.add_option("-v", "--verbose", action='store_true', dest="v", help='Verbose output (Default:False)')
    parser.add_option("--vv", "--veryverbose", action='store_true', dest="vv",
                      help='Very Verbose output (Default:False)')
    parser.add_option("--ms", "--multiple_score", action='store_true', dest="ms",
                      help='Output multiple scores (one AMR pair a score) instead of ' \
                           'a single document-level smatch score (Default: False)')
    parser.add_option('--pr', "--precision_recall", action='store_true', dest="pr",
                      help="Output precision and recall as well as the f-score. Default: false")
    parser.add_option('--justinstance', action='store_true', default=False,
                      help="just pay attention to matching instances")
    parser.add_option('--justattribute', action='store_true', default=False,
                      help="just pay attention to matching attributes")
    parser.add_option('--justrelation', action='store_true', default=False,
                      help="just pay attention to matching relations")
    parser.set_defaults(r=4, v=False, ms=False, pr=False)
    return parser
273868
def main():
    
    parser = optparse.OptionParser(usage="usage: pylon [options] input_file",
                                   version="%prog 0.4.4")

    parser.add_option("-o", "--output", dest="output", metavar="FILE",
        help="Write the solution report to FILE.")

#    parser.add_option("-q", "--quiet", action="store_true", dest="quiet",
#        default=False, help="Print less information.")

    parser.add_option("-v", "--verbose", action="store_true", dest="verbose",
        default=False, help="Print more information.")

#    parser.add_option("-g", "--gui", action="store_true", dest="gui",
#        default=False, help="Use the portable graphical interface to Pylon.")

#    parser.add_option("-n", "--no-report", action="store_true",
#        dest="no_report", default=False, help="Suppress report output.")

    parser.add_option("-d", "--debug", action="store_true", dest="debug",
        default=False, help="Print debug information.")

    parser.add_option("-t", "--input-type", dest="type", metavar="TYPE",
        default="any", help="The argument following the -t is used to "
        "indicate the format type of the input data file. The types which are "
        "currently supported include: matpower, psse [default: %default]"
        " If not specified Pylon will try to determine the type according to "
        "the file name extension and the file header.")

    parser.add_option("-s", "--solver", dest="solver", metavar="SOLVER",
        default="acpf", help="The argument following the -s is used to"
        "indicate the type of routine to use in solving. The types which are "
        "currently supported are: 'dcpf', 'acpf', 'dcopf', 'acopf', 'udopf' "
        "and 'none' [default: %default].")

    parser.add_option("-a", "--algorithm", action="store_true",
        metavar="ALGORITHM", dest="algorithm", default="newton",
        help="Indicates the algorithm type to be used for AC power flow. The "
        "types which are currently supported are: 'newton' and 'fdpf' "
        "[default: %default].")

    parser.add_option("-T", "--output-type", dest="output_type",
        metavar="OUTPUT_TYPE", default="rst", help="Indicates the output "
        "format type.  The type swhich are currently supported include: rst, "
        "matpower, csv, excel and none [default: %default].")

    (options, args) = parser.parse_args()

    if options.verbose:
        logger.setLevel(logging.INFO)
    elif options.debug:
        logger.setLevel(logging.DEBUG)
    else:
        logger.setLevel(logging.ERROR)

    # Output.
    outext = {'psse': '.raw', 'matpower': '.m'}
    if options.output:
        if options.output == "-":
            outfile = sys.stdout
            logger.setLevel(logging.CRITICAL) # must stay quiet
#            options.output_type = "none"
        else:
            outfile = open(options.output, "wb")
    elif options.output_type is not None:
        if options.output_type in outext.keys():
            inname, ext = os.path.splitext(args[0])
            outfile = inname + outext[options.output_type]
        else:
            outfile = sys.stdout
    else:
        outfile = sys.stdout
#        if not options.no_report:
#            logger.setLevel(logging.CRITICAL) # must stay quiet

    # Input.
    if len(args) > 1:
        parser.print_help()
        sys.exit(1)
    elif (len(args) == 0) or (args[0] == "-"):
        filename = ""
        if sys.stdin.isatty():
            # True if the file is connected to a tty device, and False
            # otherwise (pipeline or file redirection).
            parser.print_help()
            sys.exit(1)
        else:
            # Handle piped input ($ cat ehv3.raw | pylon | rst2pdf -o ans.pdf).
            infile = sys.stdin
    else:
        filename = args[0]
        infile = open(filename, "rb")

    if options.type == "any":
        type = detect_data_file(infile, filename)
    else:
        type = options.type

    # Get the case from the input file-like object.
    case = read_case(infile, type)

    if case is not None:
        # Routine (and algorithm) selection.
        if options.solver == "dcpf":
            solver = DCPF(case)
        elif options.solver == "acpf":
            if options.algorithm == "newton":
                solver = NewtonPF(case)
            elif options.algorithm == "fdpf":
                solver = FastDecoupledPF(case)
            else:
                logger.critical("Invalid algorithm [%s]." % options.algorithm)
                sys.exit(1)
        elif options.solver == "dcopf":
            solver = OPF(case, True)
        elif options.solver == "acopf":
            solver = OPF(case, False)
        elif options.solver == "udopf":
            solver = UDOPF(case)
        elif options.solver == "none":
            solver = None
        else:
            logger.critical("Invalid solver [%s]." % options.solver)
#            sys.exit(1)
            solver = None

        # Output writer selection.
        if options.output_type == "matpower":
            writer = MATPOWERWriter(case)
        elif options.output_type == "psse":
            writer = PSSEWriter(case)
        elif options.output_type == "rst":
            writer = ReSTWriter(case)
        elif options.output_type == "csv":
            from pylon.io.excel import CSVWriter
            writer = CSVWriter(case)
        elif options.output_type == "excel":
            from pylon.io.excel import ExcelWriter
            writer = ExcelWriter(case)
        elif options.output_type == "pickle":
            writer = PickleWriter(case)
        else:
            logger.critical("Invalid output type [%s]." % options.output_type)
            sys.exit(1)

        if solver is not None:
            solver.solve()
        if options.output_type != "none":
            writer.write(outfile)
            print('Output file {0} written'.format(outfile))
    else:
        logger.critical("Unable to read case data.")

    # Don't close stdin or stdout.
    if len(args) == 1:
        infile.close()
    if options.output and not (options.output == "-"):
        outfile.close()
529143
def main():
    """"""
    parser = get_parser()
    args = parser.parse_args()
    if hasattr(args, 'func') and args.func:
        args.func(args)
    else:
        parser.print_help()
773441
def _parser():
    '''
    
    '''
    add_arg = None
    if sys.version.startswith('2.6'):
        import optparse
        parser = optparse.OptionParser()
        add_arg = parser.add_option
    else:
        import argparse  # pylint: disable=minimum-python-version
        parser = argparse.ArgumentParser()
        add_arg = parser.add_argument

    # COMMANDS
    add_arg('-A', '--append', dest='append', action='append')
    add_arg('-D', '--delete', dest='delete', action='append')
    add_arg('-I', '--insert', dest='insert', action='append')
    add_arg('-R', '--replace', dest='replace', action='append')
    add_arg('-L', '--list', dest='list', action='append')
    add_arg('-F', '--flush', dest='flush', action='append')
    add_arg('-Z', '--zero', dest='zero', action='append')
    add_arg('-N', '--new-chain', dest='new-chain', action='append')
    add_arg('-X', '--delete-chain', dest='delete-chain', action='append')
    add_arg('-P', '--policy', dest='policy', action='append')
    add_arg('-E', '--rename-chain', dest='rename-chain', action='append')

    # PARAMETERS
    add_arg('-p', '--protocol', dest='protocol', action='append')
    add_arg('-s', '--source', dest='source', action='append')
    add_arg('-d', '--destination', dest='destination', action='append')
    add_arg('-j', '--jump', dest='jump', action='append')
    add_arg('-g', '--goto', dest='goto', action='append')
    add_arg('-i', '--in-interface', dest='in-interface', action='append')
    add_arg('-o', '--out-interface', dest='out-interface', action='append')
    add_arg('-f', '--fragment', dest='fragment', action='append')
    add_arg('-c', '--set-counters', dest='set-counters', action='append')

    # MATCH EXTENSIONS
    add_arg('-m', '--match', dest='match', action='append')
    ## addrtype
    add_arg('--src-type', dest='src-type', action='append')
    add_arg('--dst-type', dest='dst-type', action='append')
    add_arg('--limit-iface-in', dest='limit-iface-in', action='append')
    add_arg('--limit-iface-out', dest='limit-iface-out', action='append')
    ## ah
    add_arg('--ahspi', dest='ahspi', action='append')
    add_arg('--ahlen', dest='ahlen', action='append')
    add_arg('--ahres', dest='ahres', action='append')
    ## bpf
    add_arg('--bytecode', dest='bytecode', action='append')
    ## cgroup
    add_arg('--cgroup', dest='cgroup', action='append')
    ## cluster
    add_arg('--cluster-total-nodes',
            dest='cluster-total-nodes',
            action='append')
    add_arg('--cluster-local-node', dest='cluster-local-node', action='append')
    add_arg('--cluster-local-nodemask',
            dest='cluster-local-nodemask',
            action='append')
    add_arg('--cluster-hash-seed', dest='cluster-hash-seed', action='append')
    add_arg('--h-length', dest='h-length', action='append')
    add_arg('--mangle-mac-s', dest='mangle-mac-s', action='append')
    add_arg('--mangle-mac-d', dest='mangle-mac-d', action='append')
    ## comment
    add_arg('--comment', dest='comment', action='append')
    ## connbytes
    add_arg('--connbytes', dest='connbytes', action='append')
    add_arg('--connbytes-dir', dest='connbytes-dir', action='append')
    add_arg('--connbytes-mode', dest='connbytes-mode', action='append')
    ## connlabel
    add_arg('--label', dest='label', action='append')
    ## connlimit
    add_arg('--connlimit-upto', dest='connlimit-upto', action='append')
    add_arg('--connlimit-above', dest='connlimit-above', action='append')
    add_arg('--connlimit-mask', dest='connlimit-mask', action='append')
    add_arg('--connlimit-saddr', dest='connlimit-saddr', action='append')
    add_arg('--connlimit-daddr', dest='connlimit-daddr', action='append')
    ## connmark
    add_arg('--mark', dest='mark', action='append')
    ## conntrack
    add_arg('--ctstate', dest='ctstate', action='append')
    add_arg('--ctproto', dest='ctproto', action='append')
    add_arg('--ctorigsrc', dest='ctorigsrc', action='append')
    add_arg('--ctorigdst', dest='ctorigdst', action='append')
    add_arg('--ctreplsrc', dest='ctreplsrc', action='append')
    add_arg('--ctrepldst', dest='ctrepldst', action='append')
    add_arg('--ctorigsrcport', dest='ctorigsrcport', action='append')
    add_arg('--ctorigdstport', dest='ctorigdstport', action='append')
    add_arg('--ctreplsrcport', dest='ctreplsrcport', action='append')
    add_arg('--ctrepldstport', dest='ctrepldstport', action='append')
    add_arg('--ctstatus', dest='ctstatus', action='append')
    add_arg('--ctexpire', dest='ctexpire', action='append')
    add_arg('--ctdir', dest='ctdir', action='append')
    ## cpu
    add_arg('--cpu', dest='cpu', action='append')
    ## dccp
    add_arg('--sport', '--source-port', dest='source_port', action='append')
    add_arg('--dport',
            '--destination-port',
            dest='destination_port',
            action='append')
    add_arg('--dccp-types', dest='dccp-types', action='append')
    add_arg('--dccp-option', dest='dccp-option', action='append')
    ## devgroup
    add_arg('--src-group', dest='src-group', action='append')
    add_arg('--dst-group', dest='dst-group', action='append')
    ## dscp
    add_arg('--dscp', dest='dscp', action='append')
    add_arg('--dscp-class', dest='dscp-class', action='append')
    ## dst
    add_arg('--dst-len', dest='dst-len', action='append')
    add_arg('--dst-opts', dest='dst-opts', action='append')
    ## ecn
    add_arg('--ecn-tcp-cwr', dest='ecn-tcp-cwr', action='append')
    add_arg('--ecn-tcp-ece', dest='ecn-tcp-ece', action='append')
    add_arg('--ecn-ip-ect', dest='ecn-ip-ect', action='append')
    ## esp
    add_arg('--espspi', dest='espspi', action='append')
    ## frag
    add_arg('--fragid', dest='fragid', action='append')
    add_arg('--fraglen', dest='fraglen', action='append')
    add_arg('--fragres', dest='fragres', action='append')
    add_arg('--fragfirst', dest='fragfirst', action='append')
    add_arg('--fragmore', dest='fragmore', action='append')
    add_arg('--fraglast', dest='fraglast', action='append')
    ## hashlimit
    add_arg('--hashlimit-upto', dest='hashlimit-upto', action='append')
    add_arg('--hashlimit-above', dest='hashlimit-above', action='append')
    add_arg('--hashlimit-burst', dest='hashlimit-burst', action='append')
    add_arg('--hashlimit-mode', dest='hashlimit-mode', action='append')
    add_arg('--hashlimit-srcmask', dest='hashlimit-srcmask', action='append')
    add_arg('--hashlimit-dstmask', dest='hashlimit-dstmask', action='append')
    add_arg('--hashlimit-name', dest='hashlimit-name', action='append')
    add_arg('--hashlimit-htable-size',
            dest='hashlimit-htable-size',
            action='append')
    add_arg('--hashlimit-htable-max',
            dest='hashlimit-htable-max',
            action='append')
    add_arg('--hashlimit-htable-expire',
            dest='hashlimit-htable-expire',
            action='append')
    add_arg('--hashlimit-htable-gcinterval',
            dest='hashlimit-htable-gcinterval',
            action='append')
    ## hbh
    add_arg('--hbh-len', dest='hbh-len', action='append')
    add_arg('--hbh-opts', dest='hbh-opts', action='append')
    ## helper
    add_arg('--helper', dest='helper', action='append')
    ## hl
    add_arg('--hl-eq', dest='hl-eq', action='append')
    add_arg('--hl-lt', dest='hl-lt', action='append')
    add_arg('--hl-gt', dest='hl-gt', action='append')
    ## icmp
    add_arg('--icmp-type', dest='icmp-type', action='append')
    ## icmp6
    add_arg('--icmpv6-type', dest='icmpv6-type', action='append')
    ## iprange
    add_arg('--src-range', dest='src-range', action='append')
    add_arg('--dst-range', dest='dst-range', action='append')
    ## ipv6header
    add_arg('--soft', dest='soft', action='append')
    add_arg('--header', dest='header', action='append')
    ## ipvs
    add_arg('--ipvs', dest='ipvs', action='append')
    add_arg('--vproto', dest='vproto', action='append')
    add_arg('--vaddr', dest='vaddr', action='append')
    add_arg('--vport', dest='vport', action='append')
    add_arg('--vdir', dest='vdir', action='append')
    add_arg('--vmethod', dest='vmethod', action='append')
    add_arg('--vportctl', dest='vportctl', action='append')
    ## length
    add_arg('--length', dest='length', action='append')
    ## limit
    add_arg('--limit', dest='limit', action='append')
    add_arg('--limit-burst', dest='limit-burst', action='append')
    ## mac
    add_arg('--mac-source', dest='mac-source', action='append')
    ## mh
    add_arg('--mh-type', dest='mh-type', action='append')
    ## multiport
    add_arg('--sports', '--source-ports', dest='source-ports', action='append')
    add_arg('--dports',
            '--destination-ports',
            dest='destination-ports',
            action='append')
    add_arg('--ports', dest='ports', action='append')
    ## nfacct
    add_arg('--nfacct-name', dest='nfacct-name', action='append')
    ## osf
    add_arg('--genre', dest='genre', action='append')
    add_arg('--ttl', dest='ttl', action='append')
    add_arg('--log', dest='log', action='append')
    ## owner
    add_arg('--uid-owner', dest='uid-owner', action='append')
    add_arg('--gid-owner', dest='gid-owner', action='append')
    add_arg('--socket-exists', dest='socket-exists', action='append')
    ## physdev
    add_arg('--physdev-in', dest='physdev-in', action='append')
    add_arg('--physdev-out', dest='physdev-out', action='append')
    add_arg('--physdev-is-in', dest='physdev-is-in', action='append')
    add_arg('--physdev-is-out', dest='physdev-is-out', action='append')
    add_arg('--physdev-is-bridged', dest='physdev-is-bridged', action='append')
    ## pkttype
    add_arg('--pkt-type', dest='pkt-type', action='append')
    ## policy
    add_arg('--dir', dest='dir', action='append')
    add_arg('--pol', dest='pol', action='append')
    add_arg('--strict', dest='strict', action='append')
    add_arg('--reqid', dest='reqid', action='append')
    add_arg('--spi', dest='spi', action='append')
    add_arg('--proto', dest='proto', action='append')
    add_arg('--mode', dest='mode', action='append')
    add_arg('--tunnel-src', dest='tunnel-src', action='append')
    add_arg('--tunnel-dst', dest='tunnel-dst', action='append')
    add_arg('--next', dest='next', action='append')
    ## quota
    add_arg('--quota', dest='quota', action='append')
    ## rateest
    add_arg('--rateest', dest='rateest', action='append')
    add_arg('--rateest1', dest='rateest1', action='append')
    add_arg('--rateest2', dest='rateest2', action='append')
    add_arg('--rateest-delta', dest='rateest-delta', action='append')
    add_arg('--rateest-bps', dest='rateest-bps', action='append')
    add_arg('--rateest-bps1', dest='rateest-bps1', action='append')
    add_arg('--rateest-bps2', dest='rateest-bps2', action='append')
    add_arg('--rateest-pps', dest='rateest-pps', action='append')
    add_arg('--rateest-pps1', dest='rateest-pps1', action='append')
    add_arg('--rateest-pps2', dest='rateest-pps2', action='append')
    add_arg('--rateest-lt', dest='rateest-lt', action='append')
    add_arg('--rateest-gt', dest='rateest-gt', action='append')
    add_arg('--rateest-eq', dest='rateest-eq', action='append')
    add_arg('--rateest-name', dest='rateest-name', action='append')
    add_arg('--rateest-interval', dest='rateest-interval', action='append')
    add_arg('--rateest-ewma', dest='rateest-ewma', action='append')
    ## realm
    add_arg('--realm', dest='realm', action='append')
    ## recent
    add_arg('--name', dest='name', action='append')
    add_arg('--set', dest='set', action='append')
    add_arg('--rsource', dest='rsource', action='append')
    add_arg('--rdest', dest='rdest', action='append')
    add_arg('--mask', dest='mask', action='append')
    add_arg('--rcheck', dest='rcheck', action='append')
    add_arg('--update', dest='update', action='append')
    add_arg('--remove', dest='remove', action='append')
    add_arg('--seconds', dest='seconds', action='append')
    add_arg('--reap', dest='reap', action='append')
    add_arg('--hitcount', dest='hitcount', action='append')
    add_arg('--rttl', dest='rttl', action='append')
    ## rpfilter
    add_arg('--loose', dest='loose', action='append')
    add_arg('--validmark', dest='validmark', action='append')
    add_arg('--accept-local', dest='accept-local', action='append')
    add_arg('--invert', dest='invert', action='append')
    ## rt
    add_arg('--rt-type', dest='rt-type', action='append')
    add_arg('--rt-segsleft', dest='rt-segsleft', action='append')
    add_arg('--rt-len', dest='rt-len', action='append')
    add_arg('--rt-0-res', dest='rt-0-res', action='append')
    add_arg('--rt-0-addrs', dest='rt-0-addrs', action='append')
    add_arg('--rt-0-not-strict', dest='rt-0-not-strict', action='append')
    ## sctp
    add_arg('--chunk-types', dest='chunk-types', action='append')
    ## set
    add_arg('--match-set', dest='match-set', action='append')
    add_arg('--return-nomatch', dest='return-nomatch', action='append')
    add_arg('--update-counters', dest='update-counters', action='append')
    add_arg('--update-subcounters', dest='update-subcounters', action='append')
    add_arg('--packets-eq', dest='packets-eq', action='append')
    add_arg('--packets-lt', dest='packets-lt', action='append')
    add_arg('--packets-gt', dest='packets-gt', action='append')
    add_arg('--bytes-eq', dest='bytes-eq', action='append')
    add_arg('--bytes-lt', dest='bytes-lt', action='append')
    add_arg('--bytes-gt', dest='bytes-gt', action='append')
    ## socket
    add_arg('--transparent', dest='transparent', action='append')
    add_arg('--nowildcard', dest='nowildcard', action='append')
    ## state
    add_arg('--state', dest='state', action='append')
    ## statistic
    add_arg('--probability', dest='probability', action='append')
    add_arg('--every', dest='every', action='append')
    add_arg('--packet', dest='packet', action='append')
    ## string
    add_arg('--algo', dest='algo', action='append')
    add_arg('--from', dest='from', action='append')
    add_arg('--to', dest='to', action='append')
    add_arg('--string', dest='string', action='append')
    add_arg('--hex-string', dest='hex-string', action='append')
    ## tcp
    add_arg('--tcp-flags', dest='tcp-flags', action='append')
    add_arg('--syn', dest='syn', action='append')
    add_arg('--tcp-option', dest='tcp-option', action='append')
    ## tcpmss
    add_arg('--mss', dest='mss', action='append')
    ## time
    add_arg('--datestart', dest='datestart', action='append')
    add_arg('--datestop', dest='datestop', action='append')
    add_arg('--timestart', dest='timestart', action='append')
    add_arg('--timestop', dest='timestop', action='append')
    add_arg('--monthdays', dest='monthdays', action='append')
    add_arg('--weekdays', dest='weekdays', action='append')
    add_arg('--contiguous', dest='contiguous', action='append')
    add_arg('--kerneltz', dest='kerneltz', action='append')
    add_arg('--utc', dest='utc', action='append')
    add_arg('--localtz', dest='localtz', action='append')
    ## tos
    add_arg('--tos', dest='tos', action='append')
    ## ttl
    add_arg('--ttl-eq', dest='ttl-eq', action='append')
    add_arg('--ttl-gt', dest='ttl-gt', action='append')
    add_arg('--ttl-lt', dest='ttl-lt', action='append')
    ## u32
    add_arg('--u32', dest='u32', action='append')

    # Xtables-addons matches
    ## condition
    add_arg('--condition', dest='condition', action='append')
    ## dhcpmac
    add_arg('--mac', dest='mac', action='append')
    ## fuzzy
    add_arg('--lower-limit', dest='lower-limit', action='append')
    add_arg('--upper-limit', dest='upper-limit', action='append')
    ## geoip
    add_arg('--src-cc',
            '--source-country',
            dest='source-country',
            action='append')
    add_arg('--dst-cc',
            '--destination-country',
            dest='destination-country',
            action='append')
    ## gradm
    add_arg('--enabled', dest='enabled', action='append')
    add_arg('--disabled', dest='disabled', action='append')
    ## iface
    add_arg('--iface', dest='iface', action='append')
    add_arg('--dev-in', dest='dev-in', action='append')
    add_arg('--dev-out', dest='dev-out', action='append')
    add_arg('--up', dest='up', action='append')
    add_arg('--down', dest='down', action='append')
    add_arg('--broadcast', dest='broadcast', action='append')
    add_arg('--loopback', dest='loopback', action='append')
    add_arg('--pointtopoint', dest='pointtopoint', action='append')
    add_arg('--running', dest='running', action='append')
    add_arg('--noarp', dest='noarp', action='append')
    add_arg('--arp', dest='arp', action='append')
    add_arg('--promisc', dest='promisc', action='append')
    add_arg('--multicast', dest='multicast', action='append')
    add_arg('--dynamic', dest='dynamic', action='append')
    add_arg('--lower-up', dest='lower-up', action='append')
    add_arg('--dormant', dest='dormant', action='append')
    ## ipp2p
    add_arg('--edk', dest='edk', action='append')
    add_arg('--kazaa', dest='kazaa', action='append')
    add_arg('--gnu', dest='gnu', action='append')
    add_arg('--dc', dest='dc', action='append')
    add_arg('--bit', dest='bit', action='append')
    add_arg('--apple', dest='apple', action='append')
    add_arg('--soul', dest='soul', action='append')
    add_arg('--winmx', dest='winmx', action='append')
    add_arg('--ares', dest='ares', action='append')
    add_arg('--debug', dest='debug', action='append')
    ## ipv4options
    add_arg('--flags', dest='flags', action='append')
    add_arg('--any', dest='any', action='append')
    ## length2
    add_arg('--layer3', dest='layer3', action='append')
    add_arg('--layer4', dest='layer4', action='append')
    add_arg('--layer5', dest='layer5', action='append')
    ## lscan
    add_arg('--stealth', dest='stealth', action='append')
    add_arg('--synscan', dest='synscan', action='append')
    add_arg('--cnscan', dest='cnscan', action='append')
    add_arg('--grscan', dest='grscan', action='append')
    ## psd
    add_arg('--psd-weight-threshold',
            dest='psd-weight-threshold',
            action='append')
    add_arg('--psd-delay-threshold',
            dest='psd-delay-threshold',
            action='append')
    add_arg('--psd-lo-ports-weight',
            dest='psd-lo-ports-weight',
            action='append')
    add_arg('--psd-hi-ports-weight',
            dest='psd-hi-ports-weight',
            action='append')
    ## quota2
    add_arg('--grow', dest='grow', action='append')
    add_arg('--no-change', dest='no-change', action='append')
    add_arg('--packets', dest='packets', action='append')
    ## pknock
    add_arg('--knockports', dest='knockports', action='append')
    add_arg('--time', dest='time', action='append')
    add_arg('--autoclose', dest='autoclose', action='append')
    add_arg('--checkip', dest='checkip', action='append')

    # TARGET EXTENSIONS
    ## AUDIT
    add_arg('--type', dest='type', action='append')
    ## CHECKSUM
    add_arg('--checksum-fill', dest='checksum-fill', action='append')
    ## CLASSIFY
    add_arg('--set-class', dest='set-class', action='append')
    ## CLUSTERIP
    add_arg('--new', dest='new', action='append')
    add_arg('--hashmode', dest='hashmode', action='append')
    add_arg('--clustermac', dest='clustermac', action='append')
    add_arg('--total-nodes', dest='total-nodes', action='append')
    add_arg('--local-node', dest='local-node', action='append')
    add_arg('--hash-init', dest='hash-init', action='append')
    ## CONNMARK
    add_arg('--set-xmark', dest='set-xmark', action='append')
    add_arg('--save-mark', dest='save-mark', action='append')
    add_arg('--restore-mark', dest='restore-mark', action='append')
    add_arg('--and-mark', dest='and-mark', action='append')
    add_arg('--or-mark', dest='or-mark', action='append')
    add_arg('--xor-mark', dest='xor-mark', action='append')
    add_arg('--set-mark', dest='set-mark', action='append')
    add_arg('--nfmask', dest='nfmask', action='append')
    add_arg('--ctmask', dest='ctmask', action='append')
    ## CONNSECMARK
    add_arg('--save', dest='save', action='append')
    add_arg('--restore', dest='restore', action='append')
    ## CT
    add_arg('--notrack', dest='notrack', action='append')
    add_arg('--ctevents', dest='ctevents', action='append')
    add_arg('--expevents', dest='expevents', action='append')
    add_arg('--zone', dest='zone', action='append')
    add_arg('--timeout', dest='timeout', action='append')
    ## DNAT
    add_arg('--to-destination', dest='to-destination', action='append')
    add_arg('--random', dest='random', action='append')
    add_arg('--persistent', dest='persistent', action='append')
    ## DNPT
    add_arg('--src-pfx', dest='src-pfx', action='append')
    add_arg('--dst-pfx', dest='dst-pfx', action='append')
    ## DSCP
    add_arg('--set-dscp', dest='set-dscp', action='append')
    add_arg('--set-dscp-class', dest='set-dscp-class', action='append')
    ## ECN
    add_arg('--ecn-tcp-remove', dest='ecn-tcp-remove', action='append')
    ## HL
    add_arg('--hl-set', dest='hl-set', action='append')
    add_arg('--hl-dec', dest='hl-dec', action='append')
    add_arg('--hl-inc', dest='hl-inc', action='append')
    ## HMARK
    add_arg('--hmark-tuple', dest='hmark-tuple', action='append')
    add_arg('--hmark-mod', dest='hmark-mod', action='append')
    add_arg('--hmark-offset', dest='hmark-offset', action='append')
    add_arg('--hmark-src-prefix', dest='hmark-src-prefix', action='append')
    add_arg('--hmark-dst-prefix', dest='hmark-dst-prefix', action='append')
    add_arg('--hmark-sport-mask', dest='hmark-sport-mask', action='append')
    add_arg('--hmark-dport-mask', dest='hmark-dport-mask', action='append')
    add_arg('--hmark-spi-mask', dest='hmark-spi-mask', action='append')
    add_arg('--hmark-proto-mask', dest='hmark-proto-mask', action='append')
    add_arg('--hmark-rnd', dest='hmark-rnd', action='append')
    ## LED
    add_arg('--led-trigger-id', dest='led-trigger-id', action='append')
    add_arg('--led-delay', dest='led-delay', action='append')
    add_arg('--led-always-blink', dest='led-always-blink', action='append')
    ## LOG
    add_arg('--log-level', dest='log-level', action='append')
    add_arg('--log-prefix', dest='log-prefix', action='append')
    add_arg('--log-tcp-sequence', dest='log-tcp-sequence', action='append')
    add_arg('--log-tcp-options', dest='log-tcp-options', action='append')
    add_arg('--log-ip-options', dest='log-ip-options', action='append')
    add_arg('--log-uid', dest='log-uid', action='append')
    ## MASQUERADE
    add_arg('--to-ports', dest='to-ports', action='append')
    ## NFLOG
    add_arg('--nflog-group', dest='nflog-group', action='append')
    add_arg('--nflog-prefix', dest='nflog-prefix', action='append')
    add_arg('--nflog-range', dest='nflog-range', action='append')
    add_arg('--nflog-threshold', dest='nflog-threshold', action='append')
    ## NFQUEUE
    add_arg('--queue-num', dest='queue-num', action='append')
    add_arg('--queue-balance', dest='queue-balance', action='append')
    add_arg('--queue-bypass', dest='queue-bypass', action='append')
    add_arg('--queue-cpu-fanout', dest='queue-cpu-fanout', action='append')
    ## RATEEST
    add_arg('--rateest-ewmalog', dest='rateest-ewmalog', action='append')
    ## REJECT
    add_arg('--reject-with', dest='reject-with', action='append')
    ## SAME
    add_arg('--nodst', dest='nodst', action='append')
    ## SECMARK
    add_arg('--selctx', dest='selctx', action='append')
    ## SET
    add_arg('--add-set', dest='add-set', action='append')
    add_arg('--del-set', dest='del-set', action='append')
    add_arg('--exist', dest='exist', action='append')
    ## SNAT
    add_arg('--to-source', dest='to-source', action='append')
    ## TCPMSS
    add_arg('--set-mss', dest='set-mss', action='append')
    add_arg('--clamp-mss-to-pmtu', dest='clamp-mss-to-pmtu', action='append')
    ## TCPOPTSTRIP
    add_arg('--strip-options', dest='strip-options', action='append')
    ## TEE
    add_arg('--gateway', dest='gateway', action='append')
    ## TOS
    add_arg('--set-tos', dest='set-tos', action='append')
    add_arg('--and-tos', dest='and-tos', action='append')
    add_arg('--or-tos', dest='or-tos', action='append')
    add_arg('--xor-tos', dest='xor-tos', action='append')
    ## TPROXY
    add_arg('--on-port', dest='on-port', action='append')
    add_arg('--on-ip', dest='on-ip', action='append')
    add_arg('--tproxy-mark', dest='tproxy-mark', action='append')
    ## TTL
    add_arg('--ttl-set', dest='ttl-set', action='append')
    add_arg('--ttl-dec', dest='ttl-dec', action='append')
    add_arg('--ttl-inc', dest='ttl-inc', action='append')
    ## ULOG
    add_arg('--ulog-nlgroup', dest='ulog-nlgroup', action='append')
    add_arg('--ulog-prefix', dest='ulog-prefix', action='append')
    add_arg('--ulog-cprange', dest='ulog-cprange', action='append')
    add_arg('--ulog-qthreshold', dest='ulog-qthreshold', action='append')

    # Xtables-addons targets
    ## ACCOUNT
    add_arg('--addr', dest='addr', action='append')
    add_arg('--tname', dest='tname', action='append')
    ## CHAOS
    add_arg('--delude', dest='delude', action='append')
    add_arg('--tarpit', dest='tarpit', action='append')
    ## DHCPMAC
    add_arg('--set-mac', dest='set-mac', action='append')
    ## DNETMAP
    add_arg('--prefix', dest='prefix', action='append')
    add_arg('--reuse', dest='reuse', action='append')
    add_arg('--static', dest='static', action='append')
    ## IPMARK
    add_arg('--and-mask', dest='and-mask', action='append')
    add_arg('--or-mask', dest='or-mask', action='append')
    add_arg('--shift', dest='shift', action='append')
    ## TARPIT
    add_arg('--honeypot', dest='honeypot', action='append')
    add_arg('--reset', dest='reset', action='append')

    return parser