def main(argv=None):
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser(
prog="mtsv-plugin",
description="Plugins and extensions to MTSv",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.set_defaults(
timestamp=datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S'))
subparsers = parser.add_subparsers(title="commands",
metavar="COMMANDS",
help="Plugin Commands")
for command, cmd_class in COMMANDS.items():
make_sub_parser(subparsers, command, cmd_class)
# Return help if no command is passed
if len(argv) == 1:
parser.print_help(sys.stdout)
sys.exit(0)
try:
setup_and_run(argv, parser)
except KeyboardInterrupt:
error("\n-- Stopped by user --", exception=False)
def main(argv=None):
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser(
prog="mtsv-setup",
description="Download and build sequence databases and indices",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
subparsers = parser.add_subparsers(title="commands",
metavar="COMMAND",
help="Setup Commands")
for command, cmd_class in COMMANDS.items():
make_sub_parser(subparsers, command, cmd_class)
p = subparsers.add_parser("json_update")
p.add_argument("--path")
p = subparsers.add_parser("oneclick")
p = subparsers.add_parser("json_combine")
p.add_argument("--path", type=str)
p.add_argument("--custom_db", nargs='+', type=str)
p.add_argument("--partitions", type=str)
p.add_argument("--output", type=str)
p = subparsers.add_parser("ff_list")
p.add_argument("--path")
for command, cmd_class in COMMANDS.items():
for arg, desc in get_global_config(cmd_class.config_section).items():
if "_meta" in arg:
continue
if 'type' in desc:
desc['type'] = TYPES[desc['type']]
if 'default' in desc and 'help' in desc:
desc['help'] += " (default: {})".format(desc['default'])
if 'action' in desc and desc['action'] in ACTIONS:
desc['action'] = getattr(sys.modules[__name__], desc['action'])
arg = "--{}".format(arg)
if 'positional' in desc:
del desc['positional']
try:
p.add_argument(arg, **desc)
except argparse.ArgumentError:
continue
try:
add_default_arguments(p)
except argparse.ArgumentError:
pass
if len(argv) == 1:
parser.print_help(sys.stdout)
sys.exit(1)
try:
setup_and_run(parser)
except KeyboardInterrupt:
error("\n-- Stopped by user --", exception=False)
def main(argv=None):
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser(
prog="mtsv",
description="Metagenomic analysis pipeline",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.set_defaults(
timestamp=datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S'))
subparsers = parser.add_subparsers(title="commands",
metavar="COMMAND",
help="Pipeline Commands")
parser_init = subparsers.add_parser(
'init',
help="Initializes a directory with a pre-filled parameters file")
parser_init.add_argument(
"-c",
"--config",
type=TYPES['write_handle_type'],
default=DEFAULT_CFG_FNAME,
help="Specify path to write config file, "
"not required if using default config (Default: ./mtsv.cfg)")
parser_init.add_argument('-wd',
"--working_dir",
type=str,
default=os.getcwd(),
help="Specify working directory to place output. "
"(default: {})".format(os.getcwd()))
parser_init.set_defaults(cmd_class=Init)
for command, cmd_class in COMMANDS.items():
make_sub_parser(subparsers, command, cmd_class)
# Return help if no command is passed
if len(argv) == 1:
parser.print_help(sys.stdout)
sys.exit(0)
try:
setup_and_run(argv, parser)
except KeyboardInterrupt:
error("\n-- Stopped by user --", exception=False)