def add_generate_vlmc_args(parser):
add_parse_signature_args(parser)
add_distance_arguments(parser)
parser.add_argument("--condition_file",
default=None,
help="file containing the aid of the organisms to add")
)
parser.add_argument(
"--number_of_searches",
type=int,
default=0,
help="how many of the elements should be used to NN search in the tree?",
)
parser.add_argument(
"--gc_prune",
action="store_true",
help="should gc distance be used to prune the search results",
)
add_parse_signature_args(parser)
add_distance_arguments(parser)
args = parser.parse_args()
vlmcs = parse_signatures(args, "db_config.json")
print("number of vlmcs:", len(vlmcs))
distance_function = parse_distance_method(args)
tmp = args.distance_function
args.distance_function = "gc-content"
fast_dist = parse_distance_method(args)
args.distance_function = tmp
elements = [
VPTreeVLMC(vlmc, distance_function, i, fast_dist) for i, vlmc in enumerate(vlmcs)
]
if args.overlap:
if args.num: