main.py

# # from src.concerto_fp import get_biosynfoni
# # from src.tests import tsne
# import argparse

# parser = argparse.ArgumentParser(description="obtain the biosynfoni of molecule(s)")

# parser.add_argument(
#     "molecule(s)",
#     metavar="mol",
#     type=str,
#     nargs="+",
#     help="molecule representation to get biosynfoni of",
# )


# def main():
#     # required arguments -----------------------------------------------------
#     parser.add_argument(
#         "-i",
#         "--input",
#         type=str,
#         required=True,
#         help="path to molecule supplier, or smiles/InChI string if -s or - is specified.",
#     )

#     # optionals --------------------------------------------------------------
#     # --output--
#     parser.add_argument(
#         "-o",
#         "--output",
#         type=str,
#         required=False,
#         help="Path to output tsv file. If not specified, will use outfile_namer",
#     )
#     # --representation--
#     parser.add_argument(
#         "-r",
#         "--representation",
#         type=str,
#         help="specify the input type of the molecule(s). If molsupplier, choose sdf (default)",
#         action="store_true",
#         default="sdf",
#         choices=["sdf", "smiles", "inchi"],  # "sdfgz", "sdfbz2", "sdfzip"],
#     )
#     # -- coverage --
#     parser.add_argument(
#         "-c",
#         "--coverage",
#         type=bool,
#         required=False,
#         default=False,
#         help="specify if you want an output of the coverage of the biosynfoni",
#     )

#     # flags ------------------------------------------------------------------
#     parser.add_argument(
#         "--header",
#         action="store_true",
#         help="Flag to indicate that input file contains header.",
#     )


# args = parser.parse_args()
# print(args)
# # print(args.accumulate(args.integers))