def get_argument_parser():
from argparse import ArgumentParser, RawDescriptionHelpFormatter
from CallerLookup.Strings import CallerLookupArgParserHelp as s
parser = ArgumentParser(description=s.DESCRIPTION,
formatter_class=RawDescriptionHelpFormatter)
for entry in __VALID_ARGUMENTS:
arg_default_value = __DEFAULT_ARGS[entry] if entry in __DEFAULT_ARGS else None
parser.add_argument("--{0}".format(__ARG_KEYS[entry][0]),
metavar=__ARG_KEYS[entry][1].upper(),
dest=entry,
type=type(arg_default_value) if arg_default_value else None,
help=getattr(s, entry, "") + (
" (Default: {0})".format(arg_default_value) if arg_default_value else ""),
default=arg_default_value,
required=False)
return parser
python类RawDescriptionHelpFormatter()的实例源码
sam-discard-dups.py 文件源码
项目：personal-identification-pipeline
作者: TeamErlich
项目源码
文件源码
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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=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 main():
parser = argparse.ArgumentParser(description=_description(),
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-l', '--list', action='store_true')
parser.add_argument('-p', '--password')
parser.add_argument('-t', '--target-dir')
parser.add_argument('IN', type=AndroidBackup)
args = parser.parse_args()
with args.IN as infile:
if args.list:
infile.list(
password=args.password
)
else:
infile.unpack(
target_dir=args.target_dir,
password=args.password
)
def main():
parser = argparse.ArgumentParser(description=_description(),
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('OUT')
parser.add_argument('-p', '--password')
parser.add_argument('-s', '--source-dir')
parser.add_argument('-e', '--encrypt', action='store_true')
args = parser.parse_args()
ab = android_backup.AndroidBackup()
ab.version = 3
ab.compression = android_backup.CompressionType.ZLIB
ab.encryption = android_backup.EncryptionType.NONE
if args.encrypt:
ab.encryption = android_backup.EncryptionType.AES256
ab.pack(
fname=args.OUT,
source_dir=args.source_dir,
password=args.password
)
def doArchive(argv, bobRoot):
subHelp = "\n ... ".join(sorted(
[ "{:8} {}".format(c, d[1]) for (c, d) in availableArchiveCmds.items() ]))
parser = argparse.ArgumentParser(prog="bob archive",
formatter_class=argparse.RawDescriptionHelpFormatter,
description="""Manage binary artifacts archive. The following subcommands are available:
bob archive {}
""".format(subHelp))
parser.add_argument('subcommand', help="Subcommand")
parser.add_argument('args', nargs=argparse.REMAINDER,
help="Arguments for subcommand")
args = parser.parse_args(argv)
if args.subcommand in availableArchiveCmds:
availableArchiveCmds[args.subcommand][0](args.args)
else:
parser.error("Unknown subcommand '{}'".format(args.subcommand))
def main(argv=None):
if argv is None:
argv = sys.argv
parser = ArgumentParser('Level GPS phase to code.',
formatter_class=RawDescriptionHelpFormatter,
epilog=get_epilog())
parser.add_argument('leveled_arc_h5_fname',
type=str,
help='output H5 file containing leveled phase arcs')
parser.add_argument('phase_edit_h5_fname',
type=str,
help='input H5 file generated by pyrsss.gps.phase_edit')
parser.add_argument('--config',
'-c',
type=str,
nargs='+',
default=[],
help='leveling configuration overrides (specify as, e.g., minimum_elevation=15)')
args = parser.parse_args(argv[1:])
level_process(args.leveled_arc_h5_fname,
args.phase_edit_h5_fname,
config_overrides=args.config)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
CWL generator - Create GGR CWL workflows using templates
--------------------------------------------------------
'''))
# Base script options
parser.add_argument('-o', '--outdir', metavar='output_dir', dest='outdir', type=str,
help='Output directory where the files will be placed.')
parser.add_argument('-c', '--config-yaml', dest='config_yaml', required=True,
help='Config file used while rendering the CWL file.')
# Parse input
args = parser.parse_args()
if args.outdir and not os.path.isdir(args.outdir):
os.mkdir(args.outdir)
# Generate outputs
render_cwl_from_yaml(args.config_yaml, args.outdir)
def add_subparser(subparsers):
_parser = subparsers.add_parser("houston", description="QuantRocket Houston API Gateway CLI", help="quantrocket houston -h")
_subparsers = _parser.add_subparsers(title="subcommands", dest="subcommand")
_subparsers.required = True
examples = """
Ping houston.
Examples:
quantrocket houston ping
"""
parser = _subparsers.add_parser(
"ping",
help="ping houston",
epilog=examples,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.set_defaults(func="quantrocket.houston._cli_ping")
def add_subparser(subparsers):
_parser = subparsers.add_parser("license", description="QuantRocket license service CLI", help="quantrocket license -h")
_subparsers = _parser.add_subparsers(title="subcommands", dest="subcommand")
_subparsers.required = True
examples = """
Return the current license profile.
Examples:
View the current license profile:
quantrocket license get
"""
parser = _subparsers.add_parser(
"get",
help="return the current license profile",
epilog=examples,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.set_defaults(func="quantrocket.license._cli_get_license_profile")
def main():
parser = argparse.ArgumentParser(prog=os.path.basename(sys.argv[0]),
formatter_class=argparse.RawDescriptionHelpFormatter,
description=__doc__)
parser.add_argument("input",
help="XML wiki dump file")
parser.add_argument("--id", default="",
help="article number, or range first-last")
parser.add_argument("--template", action="store_true",
help="extract also all templates")
parser.add_argument("-v", "--version", action="version",
version='%(prog)s ' + version,
help="print program version")
args = parser.parse_args()
process_data(args.input, args.id, args.template)
def __init__(self, wmclass):
Gtk.Window.__init__(self)
OSDWindow._apply_css(Config())
self.argparser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=self.EPILOG)
self._add_arguments()
self.exit_code = -1
self.position = (20, -20)
self.mainloop = None
self._controller = None
self.set_name(wmclass)
self.set_wmclass(wmclass, wmclass)
self.set_decorated(False)
self.stick()
self.set_skip_taskbar_hint(True)
self.set_skip_pager_hint(True)
self.set_keep_above(True)
self.set_type_hint(Gdk.WindowTypeHint.NOTIFICATION)
def parse_args(self, method, args):
# create an argument parser
parser = ArgumentParser(prog=method.__name__,
description=dedent(method.__doc__ or ''),
formatter_class=RawDescriptionHelpFormatter)
# Add method options to the subparser
for opt in method.options:
parser.add_argument(*opt.args, **opt.kwargs)
# Add global options to the subparser
if hasattr(self, 'globals'):
for opt in self.globals:
parser.add_argument(*opt.args, **opt.kwargs)
results = {}
args = vars(parser.parse_args(args))
# Convert dashes to underscore
for key, value in args.items():
results[re.sub('-', '_', key)] = value
return results
def parseOptions():
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("inputpath", help="input.wmf file")
parser.add_argument("outputbase", nargs='?', default=None,
help="output base filename, defaults to input[.svg|.png]")
parser.add_argument("-c", "--compress", action="store_true", default=False,
help="compress SVG")
parser.add_argument("-r", "--remove", action="store_true", default=False,
help="remove input.wmf after conversion")
parser.add_argument("-v", "--verbose", action="store_true", default=False,
help="report written file type and path")
parser.add_argument('-V', '--version', action='version', version="%(prog)s (" + __version__ + ")")
parser.add_argument("--with-wmf2svg", default=WMF2SVG,
help="path to 'wmf2svg.jar' binary")
args = vars(parser.parse_args())
if not args["outputbase"]:
args["outputbase"] = os.path.splitext(args["inputpath"])[0]
return args
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input text (default: standard input).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file for BPE codes (default: standard output)")
parser.add_argument(
'--symbols', '-s', type=int, default=10000,
help="Create this many new symbols (each representing a character n-gram) (default: %(default)s))")
parser.add_argument(
'--verbose', '-v', action="store_true",
help="verbose mode.")
parser.add_argument('--min-freq', '-f', type=int, default=2, help="minimum word frequency")
return parser
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input file (default: standard input).")
parser.add_argument(
'--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
required=True,
help="File with BPE codes (created by learn_bpe.py).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file (default: standard output)")
parser.add_argument(
'--separator', '-s', type=str, default='@@', metavar='STR',
help="Separator between non-final subword units (default: '%(default)s'))")
return parser
def main():
"""Intera RSDK Joint Velocity Example: Wobbler
Commands joint velocities of randomly parameterized cosine waves
to each joint. Demonstrates Joint Velocity Control Mode.
"""
arg_fmt = argparse.RawDescriptionHelpFormatter
parser = argparse.ArgumentParser(formatter_class=arg_fmt,
description=main.__doc__)
parser.parse_args(rospy.myargv()[1:])
print("Initializing node... ")
rospy.init_node("rsdk_joint_velocity_wobbler")
wobbler = Wobbler()
rospy.on_shutdown(wobbler.clean_shutdown)
wobbler.wobble()
print("Done.")
def main():
"""RSDK Head Example: Wobbler
Nods the head and pans side-to-side towards random angles.
Demonstrates the use of the intera_interface.Head class.
"""
arg_fmt = argparse.RawDescriptionHelpFormatter
parser = argparse.ArgumentParser(formatter_class=arg_fmt,
description=main.__doc__)
parser.parse_args(rospy.myargv()[1:])
print("Initializing node... ")
rospy.init_node("rsdk_head_wobbler")
wobbler = Wobbler()
rospy.on_shutdown(wobbler.clean_shutdown)
print("Wobbling... ")
wobbler.wobble()
print("Done.")
def register_args(subparsers):
class SubcommandHelpFormatter(argparse.RawDescriptionHelpFormatter):
def _format_action(self, action):
parts = super()._format_action(action)
if action.nargs == argparse.PARSER:
parts = "\n".join([line for line in parts.split("\n")[1:]])
parts += "\n\nSpider safely!"
return parts
parser = subparsers.add_parser(name='observe',
help="Passively observe network traffic",
formatter_class=SubcommandHelpFormatter)
parser.add_argument('--list-chains', help="Prints a list of available chains",
action='store_true')
parser.add_argument('-i', '--interface', default="eth0",
help="The interface to use for the observer. (Default: eth0)")
parser.add_argument('--output', default='/dev/stdout', metavar='OUTPUTFILE',
help=("The file to output results data to. "
"Defaults to standard output."))
parser.add_argument('chains', nargs='*', help="Observer chains to use")
# Set the command entry point
parser.set_defaults(cmd=run_observer)
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input text (default: standard input).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file for BPE codes (default: standard output)")
parser.add_argument(
'--symbols', '-s', type=int, default=10000,
help="Create this many new symbols (each representing a character n-gram) (default: %(default)s))")
parser.add_argument(
'--verbose', '-v', action="store_true",
help="verbose mode.")
return parser
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input file (default: standard input).")
parser.add_argument(
'--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
required=True,
help="File with BPE codes (created by learn_bpe.py).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file (default: standard output)")
parser.add_argument(
'--separator', '-s', type=str, default='@@', metavar='STR',
help="Separator between non-final subword units (default: '%(default)s'))")
return parser
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input file (default: standard input).")
parser.add_argument(
'--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
required=True,
help="File with BPE codes (created by learn_bpe.py).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file (default: standard output)")
parser.add_argument(
'--separator', '-s', type=str, default='@@', metavar='STR',
help="Separator between non-final subword units (default: '%(default)s'))")
return parser
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input file (default: standard input).")
parser.add_argument(
'--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
required=True,
help="File with BPE codes (created by learn_bpe.py).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file (default: standard output)")
parser.add_argument(
'--separator', '-s', type=str, default='@@', metavar='STR',
help="Separator between non-final subword units (default: '%(default)s'))")
return parser
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input text (default: standard input).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file for BPE codes (default: standard output)")
parser.add_argument(
'--symbols', '-s', type=int, default=10000,
help="Create this many new symbols (each representing a character n-gram) (default: %(default)s))")
parser.add_argument(
'--verbose', '-v', action="store_true",
help="verbose mode.")
return parser
def create_parser():
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description="learn BPE-based word segmentation")
parser.add_argument(
'--input', '-i', type=argparse.FileType('r'), default=sys.stdin,
metavar='PATH',
help="Input file (default: standard input).")
parser.add_argument(
'--codes', '-c', type=argparse.FileType('r'), metavar='PATH',
required=True,
help="File with BPE codes (created by learn_bpe.py).")
parser.add_argument(
'--output', '-o', type=argparse.FileType('w'), default=sys.stdout,
metavar='PATH',
help="Output file (default: standard output)")
parser.add_argument(
'--separator', '-s', type=str, default='@@', metavar='STR',
help="Separator between non-final subword units (default: '%(default)s'))")
return parser
def main(argv, wayout):
if not len(argv):
argv.append('-h')
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
parser.add_argument("-a","--alignment", help="multiple sequence alignment", required=True)
parser.add_argument("-f","--format", default="fasta", help="alignment format [fasta]")
parser.add_argument("-g","--gap-cutoff", default=0.5, type=float, help="minimum fraction of non-gap characters per site, else is called unconserved [0.5]")
parser.add_argument("-i","--identity", action="store_true", help="report percent identity instead of score")
parser.add_argument("-p","--pdb", help="PDB format file", required=True)
parser.add_argument("-s","--sequence", help="sequence ID for PDB", required=True)
args = parser.parse_args(argv)
conservedict = get_alignment_conservation( args.alignment, args.format, args.sequence, args.gap_cutoff, args.identity)
if conservedict: # indicating that the sequence was found and something was calculated
rewrite_pdb(args.pdb, conservedict, wayout)
else:
sys.exit("# CANNOT CALCULATE CONSERVATION, EXITING")
def create_parser():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--debug', action='store_true')
parser.add_argument('--delimiter')
parser.add_argument('--embedding-size', default=200, type=int)
parser.add_argument('--graph-path')
parser.add_argument('--has-header', action='store_true')
parser.add_argument('--input', '-i', dest='infile', required=True)
parser.add_argument('--log-level', '-l', type=str.upper, default='INFO')
parser.add_argument('--num-walks', default=1, type=int)
parser.add_argument('--model', '-m', dest='model_path')
parser.add_argument('--output', '-o', dest='outfile', required=True)
parser.add_argument('--stats', action='store_true')
parser.add_argument('--undirected', action='store_true')
parser.add_argument('--walk-length', default=10, type=int)
parser.add_argument('--window-size', default=5, type=int)
parser.add_argument('--workers', default=multiprocessing.cpu_count(),
type=int)
return parser
def create_argparser():
parser = argparse.ArgumentParser(
parents=[base_parser] + tools.parsers(),
add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
group = parser.add_argument_group(
'supported compiler/build-system commands')
supported_commands = ', '.join(capture.supported_commands())
group.add_argument(
CMD_MARKER,
metavar='<cmd>',
dest='nullarg',
default=None,
help=('Command to run the compiler/build-system. '
'Supported build commands: ' + supported_commands),
)
return parser
def main() -> None:
parser = argparse.ArgumentParser(description="Smart changelog report",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("-v", "--version", help="print smartchangelog version number", action="version",
version=__version__)
parser.add_argument("-r", "--range", help="revision range (in the same meaning than git log command)")
parser.add_argument("-g", "--groupby", help="list of criteria", nargs="*")
args = parser.parse_args()
gitlog = log(revision_range=args.range)
changelog = Changelog.parse(gitlog)
if args.groupby:
criteria = tuple((Commit.property(criterion) for criterion in args.groupby))
else:
criteria = ()
node = changelog.groupby(*criteria)
print(node.report())
exit(0)
def main():
parser = argparse.ArgumentParser(prog=os.path.basename(sys.argv[0]),
formatter_class=argparse.RawDescriptionHelpFormatter,
description=__doc__)
parser.add_argument("input",
help="XML wiki dump file")
parser.add_argument("--id", default="",
help="article number, or range first-last")
parser.add_argument("--template", action="store_true",
help="extract also all templates")
parser.add_argument("-v", "--version", action="version",
version='%(prog)s ' + version,
help="print program version")
args = parser.parse_args()
process_data(args.input, args.id, args.template)
