Python get_parser 예제들

예제 #1

파일: __main__.py 프로젝트: ning-y/trcls

def main():
    r"""
    Runs trcls.
    """
    parser = cli.get_parser()
    args = parser.parse_args()
    logger = setup_logging(args)

    if args.version:
        print('trcls {}'.format(VERSION))
        exit(0)

    if args.alignment == None or args.features == None:
        logger.error(
            'Both SAM alignment and GTF annotation files must be provided')
        parser.print_help()
        exit(1)

    with open(args.features) as features_file:
        annotations = Annotations(features_file)

    with open(args.alignment) as alignment_file:
        alignments = alignment_file.readlines()

    headers = filter(lambda l: l.startswith('@'), alignments)
    headers = map(str.strip, headers)
    alignments = filter(lambda l: not l.startswith('@'), alignments)

    transcripts = get_transcripts(alignments, args.skip_tolerance,
                                  args.map_tolerance)

    print('\n'.join(headers))
    for transcript in transcripts:
        transcript.annotate(annotations, args.junction_tolerance)
        print(transcript)

예제 #2

파일: test_client.py 프로젝트: wpoely86/singularity

 def test_singularity_rootfs(self):
     '''test_singularity_rootfs ensures that --rootfs is required
     '''
     print("Testing --rootfs command...")
     parser = get_parser()
     (args, options) = parser.parse_args([])
     with self.assertRaises(SystemExit) as cm:
         run(args)
     self.assertEqual(cm.exception.code, 1)

예제 #3

파일: __main__.py 프로젝트: theonlyx/xnote

def main():
    with App() as app:
        parser = get_parser(app)
        args = parser.parse_args()
        app.config(args.config_path)
        if 'func' in args:
            args.func(args)
        else:
            parser.print_help()

예제 #4

파일: test_client.py 프로젝트: gmkurtzer/singularity

 def test_singularity_rootfs(self):
     '''test_singularity_rootfs ensures that --rootfs is required
     '''
     print("Testing --rootfs command...")
     parser = get_parser()
     (args,options) = parser.parse_args([])
     with self.assertRaises(SystemExit) as cm:
         run(args)
     self.assertEqual(cm.exception.code, 1)

예제 #5

파일: main.py 프로젝트: SonGokussj4/log-example

def main():
    parser = cli.get_parser()
    args = parser.parse_args()
    print(f">>> args: {args}")

    console = logging.StreamHandler(sys.stdout)
    if args.v == 4:
        console.setLevel(logging.TRACE)
        fmt = ColorFormatter(
            '[%(levelname)s]: %(message)s (%(filename)s:%(lineno)s)')
    elif args.v == 3:
        console.setLevel(logging.DEBUG)
        fmt = ColorFormatter(
            '[%(levelname)s]: %(message)s (%(filename)s:%(lineno)s)')
    elif args.v == 2:
        console.setLevel(logging.INFO)
        fmt = ColorFormatter('[%(levelname)s]: %(message)s')
    elif args.v == 1:
        console.setLevel(logging.WARNING)
        fmt = ColorFormatter('[%(levelname)s]: %(message)s')
    else:
        console.setLevel(logging.ERROR)
        fmt = ColorFormatter('[%(levelname)s]: %(message)s')
    console.setFormatter(fmt)
    logging.getLogger().addHandler(console)  # add to root logger

    # # Create STREAM HANDLER
    # console = logging.StreamHandler(sys.stdout)
    # console.setFormatter(fmt)
    # logging.getLogger().addHandler(console)  # add to root logger

    # log.trace(f"T MAIN Totally detailed message")
    log.info(f"E MAIN Log level: {logging.root.level}")

    add_result = add(2, 3)
    log.debug(f"D MAIN add_result: {add_result}")

    multiply_result = multiply(2, 3)
    log.info(f"I MAIN multiply_result: {multiply_result}")

예제 #6

파일: __main__.py 프로젝트: ning-y/bedshape

import logging, sys
import alias, cli, constants, profile

logging.basicConfig(format='[%(asctime)s/%(levelname)s] %(message)s')
logger = logging.getLogger('bedshape')
logger.setLevel(logging.INFO)

if __name__ == '__main__':
    root_parser, alias_parser, profile_parser = cli.get_parser()
    args = root_parser.parse_args()

    if args.which_subcommand == None:
        root_parser.print_help()
    elif args.which_subcommand == 'alias':
        alias_parser.print_help()
    elif args.which_subcommand == 'list':
        alias.list()
    elif args.which_subcommand == 'add':
        alias.add(args)
    elif args.which_subcommand == 'rm':
        alias.rm(args)
    elif args.which_subcommand == 'profile':
        profile.validate(args, profile_parser.print_help)
        profile.run(args)
    else:
        raise RuntimeError('Unrecognised subcommand.')

예제 #7

파일: data-alignment-icp-xentropy.py 프로젝트: AmirAlavi/sc-alignment-benchmarking

import embed
import alignment_task
import comparison_plots
import metrics
import runners
import cli
importlib.reload(icp)
importlib.reload(data)
importlib.reload(embed)
importlib.reload(alignment_task)
importlib.reload(comparison_plots)
importlib.reload(runners)
importlib.reload(cli)

#%%
parser = cli.get_parser()

# methods = ['None', 'MNN', 'SeuratV3', 'ScAlign', 'ICP', 'ICP2', 'ICP2_xentropy']
#arguments = '--methods SeuratV3 --datasets panc8 --input_space GENE --epochs=5 --no_standardize'
arguments = '--methods SeuratV3 --datasets panc8 --input_space GENE --epochs=10 --seurat_env_path C:\\Users\\Amir\\Anaconda3\\envs\\seuratV3'
#arguments = '--methods SeuratV3 --datasets panc8-all --input_space GENE --epochs=10 --seurat_env_path C:\\Users\\Amir\\Anaconda3\\envs\\seuratV3'
args = parser.parse_args(arguments.split())

#%%
datasets = {}
alignment_tasks = []

#%%
if 'Kowalcyzk' in args.datasets:
    datasets['Kowalcyzk'] = data.get_data('Kowalcyzk')
    embed.embed(datasets,

예제 #8

from cli import get_parser
from utils import set_logger

if __name__ == "__main__":
    set_logger()
    parser = get_parser()
    args = parser.parse_args()

    try:
        args.func(args)
    except AttributeError:
        parser.print_help()