def _main() -> None:
""" Downloads, decompresses, and compiles large databases. Also ensures
antiSMASH's module data is prepared.
"""
# Small dance to grab the antiSMASH config for the database dir.
# We don't actually want to keep anything else, but we need to load all the
# modules to make sure we can parse the file.
all_modules = antismash.get_detection_modules() + antismash.get_analysis_modules()
config = antismash.config.build_config(args=[], parser=None, isolated=True, modules=all_modules)
parser = argparse.ArgumentParser()
parser.add_argument(
"--database-dir",
default=config.database_dir,
metavar="DIR",
help="Base directory for the antiSMASH databases (default: %(default)s).",
)
args = parser.parse_args()
download(args)
try:
antismash.main.prepare_module_data()
except Exception as err: # pylint: disable=broad-except
print("Error encountered while preparing module data:", str(err), file=sys.stderr)
sys.exit(1)
def main(args):
all_modules = antismash.get_detection_modules(
) + antismash.get_analysis_modules()
parser = antismash.config.args.build_parser(from_config_file=True,
modules=all_modules)
# if --help, show help texts and exit
if set(args).intersection({"-h", "--help", "--help-showall"}):
parser.print_help(None, "--help-showall" in args)
return 0
options = antismash.config.build_config(args, parser=parser)
if options.write_config_file:
parser.write_to_config_file(options.write_config_file,
options.__dict__)
return 0
# if -V, show version text and exit
if options.version:
print("antiSMASH %s" % get_version())
return 0
if len(options.sequences) > 1:
parser.error("Only one sequence file should be provided")
return 1
if len(options.sequences) < 1 and not options.reuse_results \
and not options.check_prereqs_only and not options.list_plugins:
parser.error(
"One of an input file or --reuse-results must be specified")
return 1
if options.sequences and options.reuse_results:
parser.error("Provide a sequence file or results to reuse, not both.")
return 1
if options.sequences:
sequence = options.sequences[0]
options.__dict__.pop("sequences")
else:
sequence = ""
options.version = get_version()
return antismash.run_antismash(sequence, options)