def generate_argparser():
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
epilog=LICENSE)
parser.add_argument('-d', '--nodedata', required=True, nargs=1,
help=("file containing paths of one or more"
"RESULT.node.score.csv files"))
parser.add_argument('-t', '--tree', required=True, type=open,
nargs=1,
help="tree file in Newick format")
parser.add_argument('-o', '--out', required=True,
nargs=1,
help="new output files prefix")
parser.add_argument("-v", "--verbose", action="store_true")
# These args are hidden to pass through to the treedata object
parser.add_argument("-c", "--clade", nargs=1, help=argparse.SUPPRESS)
parser.add_argument("-s", "--startk", type=int, default=0,
help=argparse.SUPPRESS)
parser.add_argument("-p", "--stopk", type=int, help=argparse.SUPPRESS)
return parser
python类ArgumentParser()的实例源码
def parse_args():
parser = argparse.ArgumentParser(description='Backup Block Device')
parser.add_argument('--backup', required=True,
help='Path to backup file or device')
parser.add_argument('--manifest', required=True,
help='manifest file')
parser.add_argument('--cbt', required=False,
help='change block tracking info')
parser.add_argument('--backend', required=False, default='raw',
choices=['raw'], help='backend driver')
parser.add_argument('--storage', required=False, default='local',
choices=['local'], help='storage driver')
parser.add_argument('--location', required=True, help='storage path')
parser.add_argument('--driver', required=False, default='sqlite',
choices=['osdk', 'sqlite'], help='manifest driver')
return parser.parse_args()
def main():
"""Entry point for creating an application specific security group"""
logging.basicConfig(format=LOGGING_FORMAT)
log = logging.getLogger(__name__)
parser = argparse.ArgumentParser()
add_debug(parser)
add_app(parser)
add_env(parser)
add_properties(parser)
add_region(parser)
args = parser.parse_args()
logging.getLogger(__package__.split('.')[0]).setLevel(args.debug)
log.debug('Parsed arguments: %s', args)
spinnakerapps = SpinnakerSecurityGroup(app=args.app, env=args.env, region=args.region, prop_path=args.properties)
spinnakerapps.create_security_group()
def main():
arg_parser = argparse.ArgumentParser(description='A Utility to convert Natural Language to SQL query')
arg_parser.add_argument('-d', '--database', help='Path to SQL dump file', required=True)
arg_parser.add_argument('-l', '--language', help='Path to language configuration file', required=True)
arg_parser.add_argument('-i', '--sentence', help='Input sentence to parse', required=True)
arg_parser.add_argument('-j', '--json_output', help='path to JSON output file', default=None)
arg_parser.add_argument('-t', '--thesaurus', help='path to thesaurus file', default=None)
arg_parser.add_argument('-s', '--stopwords', help='path to stopwords file', default=None)
args = arg_parser.parse_args()
ln2sql = Ln2sql(
database_path=args.database,
language_path=args.language,
json_output_path=args.json_output,
thesaurus_path=args.thesaurus,
stopwords_path=args.stopwords,
).get_query(args.sentence)
def _parse_args(args):
parser = argparse.ArgumentParser()
if any([arg == '--version' for arg in args]):
return argparse.Namespace(version=True)
parser.add_argument('script', help='Script to run')
parser.add_argument('target', nargs='?', default='build', help='Target object to build; defaults to \'build\'')
parser.add_argument('--version', action='store_true', help='Print version info and exit')
parser.add_argument('--clear', action='store_true', help='Clear output directory')
parser.add_argument('--clear-cache', action='store_true', help='Clear cache before compiling')
parser.add_argument('--threads', '-t', type=int, help='Set thread count; defaults to cores*2')
parser.add_argument('--no-threading', '-nt', action='store_true', help='Disable multithreaded compiling')
# TODO: Make target '*' instead of '?' so multiple targets could be ran from the same command
return parser.parse_args(args)
def ask_user(preferences = {}):
def add_argument(name, help, **kwargs):
kwargs['required'] = kwargs.get('required', not (name in preferences))
kwargs['default'] = kwargs.get('default', preferences.get(name, None))
parser.add_argument('--' + name, help=help, **kwargs)
parser = argparse.ArgumentParser(description="Access MeuAlelo system to extract this month's operations")
add_argument('cpf', "CPF with only numbers")
add_argument('password', "Password used to access the system")
add_argument('card', "Which card from the list we want to access", type=int, default=0)
add_argument('save', "If present saves the provided configurations in an init file",
required=False, action="store_true")
add_argument('month', "Specify for which month transactions must be converted",
required=False, type=int)
return vars(parser.parse_args())
def parse_min_args():
# Parse arguments
parser = ArgumentParser()
parser.add_argument('--expname', '-e', dest='exp', metavar='e', type=str,
default='dev', help='Name of the experiment to be run.')
parser.add_argument('--n_steps', dest='n_steps', type=int,
default=300, help='Number of updates to be performed.')
parser.add_argument('--n_test_iter', dest='n_test_iter', type=int,
default=100, help='Number of episodes to test on.')
parser.add_argument('--update_frequency', dest='update_frequency', type=int,
default=1500, help='Number of steps before updating parameters.')
parser.add_argument('--max_path_length', dest='max_path_length', type=int,
default=15000, help='Max length for a trajectory/episode.')
parser.add_argument('--print_interval', dest='print_interval', type=int,
default=1000, help='Number of steps between each print summary.')
parser.add_argument('--record', dest='record', type=bool,
default=False, help='Whether to record videos at test time.')
parser.add_argument('--render', dest='render', type=bool,
default=False, help='Whether to render display at train time.')
return parser.parse_args()
def main():
import argparse
logger = logging.getLogger(__name__)
logger.setLevel(logging.DEBUG)
logger.addHandler(logging.StreamHandler(sys.stdout))
parser = argparse.ArgumentParser(description="Linux distro info tool")
parser.add_argument(
'--json',
'-j',
help="Output in machine readable format",
action="store_true")
args = parser.parse_args()
if args.json:
logger.info(json.dumps(info(), indent=4, sort_keys=True))
else:
logger.info('Name: %s', name(pretty=True))
distribution_version = version(pretty=True)
if distribution_version:
logger.info('Version: %s', distribution_version)
distribution_codename = codename()
if distribution_codename:
logger.info('Codename: %s', distribution_codename)
def get_args():
parser = ArgumentParser(
description="Investigate nucleotide composition and base quality.")
parser.add_argument("-v", "--version",
help="Print version and exit.",
action="version",
version='NanoQC {}'.format(__version__))
parser.add_argument("--outdir",
help="Specify directory in which output has to be created.",
default=".")
parser.add_argument("-f", "--format",
help="Specify the output format of the plots.",
default="png",
type=str,
choices=['eps', 'jpeg', 'jpg', 'pdf', 'pgf', 'png', 'ps',
'raw', 'rgba', 'svg', 'svgz', 'tif', 'tiff'])
parser.add_argument("fastq",
help="Reads data in fastq format.")
return parser.parse_args()
def __init__(self, base_path):
"""
Initialize CLI arguments
"""
parser = argparse.ArgumentParser(
description='Check dependencies by recipe.')
parser.add_argument('action', choices=['get', 'install', 'check'],
default='check', nargs=1,
help='get: Download recipe from Gist; \ninstall: '
'Trying to install newer package versions; '
'\ncheck: Simple check')
parser.add_argument('param', nargs='?',
help='Custom recipe directory or gist ID '
'to download recipe')
parser.add_argument("-v", "--verbose", action="store_true",
help="With this flag you can see on the display"
"(not in the log file) "
"triggered command output.")
self.__cli_args = parser.parse_args()
self.__base_path = base_path
def kas_get_argparser():
"""
Creates a argparser for kas with all plugins.
"""
parser = argparse.ArgumentParser(description='kas - setup tool for '
'bitbake based project')
verstr = '%(prog)s {} (configuration format version {}, ' \
'earliest compatible version {})'.format(__version__, __file_version__,
__compatible_file_version__)
parser.add_argument('--version', action='version', version=verstr)
parser.add_argument('-d', '--debug',
action='store_true',
help='Enable debug logging')
subparser = parser.add_subparsers(help='sub command help', dest='cmd')
for ext_plugin in pkg_resources.iter_entry_points('kas.plugins'):
ext_plugin.load()
for plugin in getattr(kasplugin, 'plugins', []):
plugin.get_argparser(subparser)
return parser
def main():
import argparse
logger = logging.getLogger(__name__)
logger.setLevel(logging.DEBUG)
logger.addHandler(logging.StreamHandler(sys.stdout))
parser = argparse.ArgumentParser(description="Linux distro info tool")
parser.add_argument(
'--json',
'-j',
help="Output in machine readable format",
action="store_true")
args = parser.parse_args()
if args.json:
logger.info(json.dumps(info(), indent=4, sort_keys=True))
else:
logger.info('Name: %s', name(pretty=True))
distribution_version = version(pretty=True)
if distribution_version:
logger.info('Version: %s', distribution_version)
distribution_codename = codename()
if distribution_codename:
logger.info('Codename: %s', distribution_codename)
def test_main(args):
""" """
parser = argparse.ArgumentParser(description=description())
parser.add_argument('-f',
'--image_file',
default='../examples/GodRoss.jpg',
type=str,
help='The file path of the image to test')
parser.add_argument('test_name',
type=str,
help='The name of the test to perform')
args = parser.parse_args(args)
try:
if args.test_name == "test_many_random":
test_many_random(args.image_file, 5, 5)
elif args.test_name == "test_multi_origin":
test_multi_origin(args.image_file, 4)
else: print("Error: Test function {} doesn't exist".format(args.test_name),
file=sys.stderr)
except OSError:
print("Error: File: {} doesn't exist".format(args.image_file),
file=sys.stderr)
def get_args():
"""
Return Command Line Arguments.
:return: ArgumentParser instance
"""
parser = ArgumentParser(description="vSphere Ansible Inventory.",
epilog="Example:\n"
"./vsphere_inventory.py -l\n"
"./vsphere_inventory.py -s <vSphere.hostname>"
"-u <vSphere_username> -p <vSphere_password> -l\n")
parser.add_argument('-s', '--hostname', help='vSphere vCenter FQDN')
parser.add_argument('-u', '--username', help='vSphere username')
parser.add_argument('-p', '--password', help='vSphere password')
parser.add_argument('-P', '--port', help='vSphere Port')
parser.add_argument('-c', '--no_cert_check', help='Dont check vSphere certificate', action='store_true')
parser.add_argument('-g', '--guest', help='Print a single guest')
parser.add_argument('-x', '--host', help='Print a single guest')
parser.add_argument('-r', '--reload-cache', help='Reload cache', action='store_true')
parser.add_argument('-l', '--list', help='List all VMs', action='store_true')
return parser.parse_args()
def main():
"""
Runtime management of the CTF API
"""
parser = ArgumentParser(description="CTF API configuration")
parser.add_argument("-v", "--verbose", action="count", help="increase verbosity", default=0)
parser.add_argument("-p", "--port", action="store", help="port the server should listen on.", type=int, default=8000)
parser.add_argument("-l", "--listen", action="store", help="host the server should listen on.", default="0.0.0.0")
parser.add_argument("-d", "--debug", action="store_true", help="run the server in debug mode.", default=False)
parser.add_argument("-k", "--debug-key", action="store", help="debug key for problem grading; only applies if debug is enabled", type=str, default=None)
args = parser.parse_args()
if args.debug:
api.problem.DEBUG_KEY = args.debug_key
keyword_args, _ = object_from_args(args)
api.app.config_app().run(host=args.listen, port=args.port, debug=args.debug)
sam-discard-dups.py 文件源码
项目:personal-identification-pipeline
作者: TeamErlich
项目源码
文件源码
阅读 29
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def parse_command_line():
# Define parameters
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="SAM - Discard duplicates/multiple-mappers",
version=version_info,
epilog="""
This script reads a SAM file, and discards ALL reads which map
multiple times (does not keep even one of the mapping locations).
TODO: Explain hard-clipped reads in minION runs
Example:
# Remove all duplicated reads dirnames:
$ %(prog)s input.sam > output.no-dups.sam
""")
# Positional parameter
parser.add_argument('filename', metavar='FILE', help='file to process');
args = parser.parse_args()
return args
def main():
parser = argparse.ArgumentParser(description='FractalNet on CIFAR-100')
parser.add_argument('--load', nargs=1,
help='Test network with weights file')
parser.add_argument('--deepest', help='Build with only deepest column activated',
action='store_true')
parser.add_argument('--test-all', nargs=1,
help='Test all the weights from a folder')
parser.add_argument('--summary',
help='Print a summary of the network and exit',
action='store_true')
args = parser.parse_args()
net = build_network(deepest=args.deepest)
if args.load:
weights = args.load[0]
test_network(net, weights)
elif args.test_all:
folder = args.test_all[0]
for weights in glob.glob(os.path.join(folder, 'weigh*')):
test_network(net, weights)
elif args.summary:
net.summary()
else:
train_network(net)
def main():
parser = argparse.ArgumentParser(description='FractalNet on CIFAR-10')
parser.add_argument('--load', nargs=1,
help='Test network with weights file')
parser.add_argument('--deepest', help='Build with only deepest column activated',
action='store_true')
parser.add_argument('--test-all', nargs=1,
help='Test all the weights from a folder')
parser.add_argument('--summary',
help='Print a summary of the network and exit',
action='store_true')
args = parser.parse_args()
net = build_network(deepest=args.deepest)
if args.load:
weights = args.load[0]
test_network(net, weights)
elif args.test_all:
folder = args.test_all[0]
for weights in glob.glob(os.path.join(folder, 'weigh*')):
test_network(net, weights)
elif args.summary:
net.summary()
else:
train_network(net)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--weights', default="YOLO_small.ckpt", type=str)
parser.add_argument('--data_dir', default="data", type=str)
parser.add_argument('--threshold', default=0.2, type=float)
parser.add_argument('--iou_threshold', default=0.5, type=float)
parser.add_argument('--gpu', default='', type=str)
args = parser.parse_args()
if args.gpu is not None:
cfg.GPU = args.gpu
if args.data_dir != cfg.DATA_PATH:
update_config_paths(args.data_dir, args.weights)
os.environ['CUDA_VISIBLE_DEVICES'] = cfg.GPU
yolo = YOLONet()
pascal = pascal_voc('train')
solver = Solver(yolo, pascal)
print('Start training ...')
solver.train()
print('Done training.')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--weights', default="YOLO_small.ckpt", type=str)
parser.add_argument('--weight_dir', default='weights', type=str)
parser.add_argument('--data_dir', default="data", type=str)
parser.add_argument('--gpu', default='', type=str)
args = parser.parse_args()
os.environ['CUDA_VISIBLE_DEVICES'] = args.gpu
yolo = YOLONet(False)
weight_file = os.path.join(args.data_dir, args.weight_dir, args.weights)
detector = Detector(yolo, weight_file)
# detect from camera
# cap = cv2.VideoCapture(-1)
# detector.camera_detector(cap)
# detect from image file
imname = 'test/person.jpg'
detector.image_detector(imname)
def _cli_parse(args): # pragma: no coverage
from argparse import ArgumentParser
parser = ArgumentParser(usage="usage: %sprog [options] package.module:app")
opt = parser.add_argument
opt('app', help='WSGI app entry point.')
opt("--version", action="store_true", help="show version number.")
opt("-b", "--bind", metavar="ADDRESS", help="bind socket to ADDRESS.")
opt("-s", "--server", default='wsgiref', help="use SERVER as backend.")
opt("-p", "--plugin", action="append", help="install additional plugin/s.")
opt("-c", "--conf", action="append", metavar="FILE",
help="load config values from FILE.")
opt("-C", "--param", action="append", metavar="NAME=VALUE",
help="override config values.")
opt("--debug", action="store_true", help="start server in debug mode.")
opt("--reload", action="store_true", help="auto-reload on file changes.")
cli_args = parser.parse_args(args)
return cli_args, parser
def read_options(fnc, **kwargs):
"""Parse an argparse parser and return an array
Args:
fnc (TYPE): Description
**kwargs: Description
Returns:
TYPE: Description
"""
if isinstance(fnc.__call__(), argparse.ArgumentParser):
# print argparse2json.convert(fnc.__call__())['widgets']['primary']['contents']
datas = argparse2json.convert(fnc.__call__())['widgets']['primary']['contents']
options = []
for data in datas:
opts_list = {}
# print json.dumps(data['data'])
opts_list['option'] = data['data']
options.append(opts_list)
# print 'options', json.dumps(options)
return options
def main():
parser = argparse.ArgumentParser(description=help_msg(
), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-v', '--version',
help='Show the version and exit', action="store_true")
parser.add_argument(
'-d', '--debug', help='Increase verbosity to ease debugging process', action="store_true")
parser.add_argument('-t', '--tree', nargs=1, dest='acbs_tree', help='Specify which abbs-tree to use')
parser.add_argument('packages', nargs='*', help='Packages to be built')
args = parser.parse_args()
if args.version:
print('ACBS version {}'.format(acbs_version))
if len(args.packages) > 0:
if args.acbs_tree is not None:
init_env(args.acbs_tree)
else:
init_env()
sys.exit(build_pkgs(args.packages))
def parse_args():
parser = argparse.ArgumentParser(
description="data_pipeline_introspector provides ability to view the current "
"state of the data pipeline from a top-down view of namespaces."
)
parser.add_argument(
'--version',
action='version',
version="data_pipeline {}".format(__version__)
)
subparsers = parser.add_subparsers()
ListCommandParser.add_parser(subparsers)
InfoCommandParser.add_parser(subparsers)
RegisterCommandParser.add_parser(subparsers)
SchemaCheckCommand.add_parser(subparsers)
return parser.parse_args()
def generate_argparser():
"""Generates the argparsr ArgumentParser
"""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
epilog=LICENSE)
parser.add_argument('-t', '--tree', type=open, nargs=1,
help="input tree in newick format")
parser.add_argument('-d', '--data', type=os.path.abspath, nargs=1,
help=("CSV output from quartet_sampling"
" (RESULT.node.score.csv)"))
parser.add_argument("-c", "--clade", nargs=1, help=argparse.SUPPRESS)
parser.add_argument("-v", "--verbose", action="store_true",
help="verbose screen output")
parser.add_argument("-s", "--startk", type=int, default=0,
help=argparse.SUPPRESS)
parser.add_argument("-p", "--stopk", type=int, help=argparse.SUPPRESS)
return parser
def generate_argparser():
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
epilog=LICENSE)
parser.add_argument('-d', '--data', type=os.path.abspath, nargs=1,
required=True,
help=("RESULT.node.score.csv file output from"
"quartet_sampling.py"))
parser.add_argument("-c", "--clade", nargs=1,
help=("specify a clade using a comma-separated"
"list of 2+ descendant taxa"))
parser.add_argument("-v", "--verbose", action="store_true",
help="verbose screen output")
parser.add_argument("-s", "--startk", type=int, default=0,
help="starting branch numerical index")
parser.add_argument("-p", "--stopk", type=int,
help="stopping branch numerical index")
parser.add_argument("-o", "--out", type=os.path.abspath, nargs=1,
help="output file path for statistics")
return parser
def _main(argv=None):
parser = argparse.ArgumentParser(prog="python -m ensurepip._uninstall")
parser.add_argument(
"--version",
action="version",
version="pip {}".format(ensurepip.version()),
help="Show the version of pip this will attempt to uninstall.",
)
parser.add_argument(
"-v", "--verbose",
action="count",
default=0,
dest="verbosity",
help=("Give more output. Option is additive, and can be used up to 3 "
"times."),
)
args = parser.parse_args(argv)
ensurepip._uninstall_helper(verbosity=args.verbosity)
def main():
argparser = argparse.ArgumentParser()
argparser.add_argument("command",
help="command to invoke: preview or build")
argparser.add_argument("file",
help="File to proceed",
default="index.qq",
nargs='?')
argparser.add_argument("--node-mathjax",
help="Use server-side mathjax",
action='store_true')
argparser.add_argument('--base-url',
help="Base URL")
argparser.add_argument('--copy-mathjax',
help='Copy mathjax files to build/assets',
action="store_true")
args = argparser.parse_args()
app.config['FILE'] = args.file
if args.command in commands:
commands[args.command](**vars(args))
else:
print("Unknown command " + args.command)
def analyze_command(args):
parser = argparse.ArgumentParser(description='Analyzes indexes FCC comments')
parser.add_argument(
'--endpoint', dest='endpoint',
default=os.environ.get('ES_ENDPOINT', 'http://127.0.0.1:9200/')
)
parser.add_argument(
'--no-verify', dest='verify', nargs='?',
help='Don\'t verify SSL certs', default=True,
const=False
)
parser.add_argument(
'--limit', dest='limit',
default=10000
)
command_args = parser.parse_args(args=args)
analyzer = CommentAnalyzer(**vars(command_args))
analyzer.run()
def add_result_config():
session = make_session()
parser = argparse.ArgumentParser()
parser.add_argument("league", type=int, help="league id")
parser.add_argument("match", type=int, help="match id")
args = parser.parse_args()
results = results_config
with transaction.manager:
for team in results:
for player in team['players']:
result_string = "%s,%s" % (team["position"], player["kills"])
hero_id = session.query(Hero).filter(Hero.league == args.league).filter(Hero.name == player['name']).first()
if not hero_id:
print "Name wrong"
return
session.add(Result(args.league, hero_id.id, args.match, result_string,
time.time(), 1, 1))
transaction.commit()
return