def run_subtool(parser, args):
logger.debug(f"command: {args.command}")
logger.debug(f"args: {args}")
if args.command == "variants":
if args.sub_command == "add":
from mykrobe.cmds.variants.add import run
elif args.sub_command == "dump-probes":
from mykrobe.cmds.dump import run
elif args.sub_command == "make-probes":
from mykrobe.cmds.makeprobes import run
elif args.command == "predict":
from mykrobe.cmds.amr import run
elif args.command == "panels":
if args.sub_command == "describe":
from mykrobe.cmds.panels import describe as run
elif args.sub_command == "update_metadata":
from mykrobe.cmds.panels import update_metadata as run
elif args.sub_command == "update_species":
from mykrobe.cmds.panels import update_species as run
elif args.command == "genotype":
raise NotImplementedError(
"The 'genotype' option is no longer available - please use 'predict' with "
"the species as 'custom' and the option --custom_probe_set_path "
"probes.fasta (and also see the options --custom_variant_to_resistance_json, "
"--custom_lineage_json) "
)
else:
raise NotImplementedError(f"{args.command} is not a recognised mykrobe command")
# run the chosen submodule.
logger.debug(f"Start run {run.__module__}")
run(parser, args)
logger.debug(f"End run {run.__module__}")
def run_subtool(parser, args):
if args.command == "variants":
if args.sub_command == 'add':
from mykrobe.cmds.variants.add import run
# elif args.command == "add-gt":
# from mykrobe.cmds.atlasadd import run
elif args.sub_command == "dump-probes":
from mykrobe.cmds.dump import run
elif args.sub_command == "make-probes":
from mykrobe.cmds.makeprobes import run
elif args.command == "predict":
from mykrobe.cmds.amr import run
elif args.command == "genotype":
from mykrobe.cmds.genotype import run
elif args.command == "place":
from mykrobe.cmds.place import run
elif args.command == "diff":
from mykrobe.cmds.diff import run
# run the chosen submodule.
run(parser, args)