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)
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)
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()
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)
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}")
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.')
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,
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()