comparison calculate_pore_diameter_aqp.py @ 12:066606280457 draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 39e6c57933401793343e38ebe55ad3cc52a3112d"

11:a4097272ade0

        "--verbose",
        action="store_true",
        help="""Information messages to stderr""",
    )
    parser.add_argument(
        "-gro", "--gro_file", type=str, nargs=1, help="""My input .gro file"""
    )
    parser.add_argument(
        "-xtc", "--xtc_file", type=str, nargs=1, help="""My input .xtc file"""
    )
    parser.add_argument(
        "--gro_file_ext", type=str, nargs=1, help="""My input .gro file"""
    )
    parser.add_argument(
        "--xtc_file_ext", type=str, nargs=1, help="""My input .xtc file"""
    )
    parser.add_argument(
        "-w", "--work_directory", type=str, default="./",
        help="""It's work Directory"""
    )
    parser.add_argument(
        "-od",
        "--output_directory",
        default="stdout",
        type=str,
        nargs=1,
        help="""It's output Directory""",
    )
    parser.add_argument(

        default="",
        nargs=1,
        help="""3-letter pattern of the 4 amino acids of second ArR on HE""",
    )
    parser.add_argument("-o", "--output", help="""Output for files""")
    parser.add_argument("-log", "--log_output", help="""Output for files""")
    return parser.parse_args()


def search_amino_acids_pattern(list_pattern, uni):
    """

# Class


if __name__ == "__main__":
    args = parse_arguments()
    out_file_name = "test"
    file_name_log = out_file_name + ".log"
    if args.verbose:
        if args.log_output:
            if os.path.isfile(args.log_output):
                os.remove(args.log_output)
            logging.basicConfig(
                filename=args.log_output,
                format="%(levelname)s - %(message)s",
                level=logging.INFO,
            )
        else:
            if os.path.isfile(file_name_log):
                os.remove(file_name_log)
            logging.basicConfig(
                filename=file_name_log,
                format="%(levelname)s - %(message)s",
                level=logging.INFO,
            )
        logging.info("verbose mode on")
    gro_file = ''
    xtc_file = ''
    if args.gro_file:
        gro_file = os.path.basename(args.gro_file[0])
    else:
        logging.critical("A .gro file must be provided")
    if args.xtc_file:
        xtc_file = os.path.basename(args.xtc_file[0])
    else:
        logging.critical("A .xtc file must be provided")
    if args.work_directory:
        work_directory = args.work_directory[0]
    else:
        work_directory = os.path.dirname(args.gro_file[0])
        if not work_directory.endswith("/"):
            work_directory += "/"
    output_directory = args.output_directory[0]
    if args.output:
        output = args.output
    else:
        output = ""
    os.chdir(work_directory)
    if args.gro_file_ext and args.xtc_file_ext:
        u = Mda.Universe(
            args.gro_file[0],
            args.xtc_file[0],
            topology_format=args.gro_file_ext[0],
            format=args.xtc_file_ext[0],
        )
    else:
        u = Mda.Universe(args.gro_file[0], args.xtc_file[0])
    if args.verbose:
        logging.info("Load universe : " + str(u))
    if args.npa_one:
        resid_npa1 = args.npa_one[0].split()
    else:
        resid_npa1 = args.npa_one
    if args.npa_second:
        resid_npa2 = args.npa_second[0].split()
    else:
        resid_npa2 = args.npa_second
    if args.arr_one:
        resid_arr1 = args.arr_one[0].split()
    else:
        resid_arr1 = args.arr_one
    if args.arr_second:
        resid_arr2 = args.arr_second[0].split()
    else:
        resid_arr2 = args.arr_second
    df_final = create_final_dataframe(resid_arr1, resid_arr2,
                                      resid_npa1, resid_npa2, u)
    if len(output_directory) > 2:
        try:
            os.makedirs(output_directory, exist_ok=True)

            print("Directory '%s' can not be created")
        os.chdir(output_directory)
    if len(output) > 2:
        df_final.to_csv(output, sep="\t", index=False)
    else:
        file_name_tabular = out_file_name + "PairDist.tabular"
        df_final.to_csv(file_name_tabular, sep="\t", index=False)

12:066606280457

        "--verbose",
        action="store_true",
        help="""Information messages to stderr""",
    )
    parser.add_argument(
        "-gro", "--gro_file", type=str, help="""My input .gro file"""
    )
    parser.add_argument(
        "-xtc", "--xtc_file", type=str, help="""My input .xtc file"""
    )
    parser.add_argument(
        "--gro_file_ext", type=str, help="""My input .gro file"""
    )
    parser.add_argument(
        "--xtc_file_ext", type=str, help="""My input .xtc file"""
    )
    parser.add_argument(
        "-w", "--work_directory", type=str, default="./",
        help="""It's work Directory"""
    )
    parser.add_argument(
        "-od",
        "--output_directory",
        default="out/",
        type=str,
        nargs=1,
        help="""It's output Directory""",
    )
    parser.add_argument(

        default="",
        nargs=1,
        help="""3-letter pattern of the 4 amino acids of second ArR on HE""",
    )
    parser.add_argument("-o", "--output", help="""Output for files""")
    parser.add_argument("-log", "--log_output",
                        default="log/calculate_pore_diameter_aqp.log",
                        help="""Output for files""")
    return parser.parse_args()


def search_amino_acids_pattern(list_pattern, uni):
    """

# Class


if __name__ == "__main__":
    args = parse_arguments()
    if args.verbose:
        if len(os.path.dirname(args.log_output)) > 1:
            log_dir = os.path.dirname(args.log_output)
        else:
            log_dir = "log/"
        try:
            os.makedirs(log_dir, exist_ok=True)
        except OSError:
            print("Directory '%s' can not be created")
        if os.path.isfile(args.log_output):
            os.remove(args.log_output)
        logging.basicConfig(
            filename=args.log_output,
            format="%(levelname)s - %(message)s",
            level=logging.INFO,
        )
        logging.info("verbose mode on")
    gro_file = ''
    xtc_file = ''
    if args.gro_file:
        gro_file = os.path.basename(args.gro_file)
        if ".gro" not in gro_file:
            if args.verbose:
                logging.critical("-gro error: input is not .gro file")
            print("-gro error: input is not .gro file")
            sys.exit(1)
    else:
        if args.verbose:
            logging.critical("A .gro file must be provided")
        print("A .gro file must be provided")
        sys.exit(1)
    if args.xtc_file:
        xtc_file = os.path.basename(args.xtc_file)
        if ".xtc" not in xtc_file:
            if args.xtc_file_ext == "xtc":
                xtc_file = xtc_file + ".xtc"
            else:
                if args.verbose:
                    logging.critical("-xtc error: input is not .xtc file")
                print("-xtc error: input is not .xtc file")
                sys.exit(1)
    else:
        if args.verbose:
            logging.critical("A .xtc file must be provided")
        print("A .xtc file must be provided")
        sys.exit(1)
    if len(os.path.dirname(args.gro_file)) > 1:
        work_directory = os.path.dirname(args.gro_file)
    else:
        work_directory = args.work_directory
    if not work_directory.endswith("/"):
        work_directory += "/"
    output_directory = args.output_directory
    if args.output:
        output = args.output
    else:
        output = ""
    os.chdir(work_directory)
    if args.gro_file_ext and args.xtc_file_ext:
        u = Mda.Universe(
            args.gro_file,
            args.xtc_file,
            topology_format=args.gro_file_ext,
            format=args.xtc_file_ext,
        )
    else:
        u = Mda.Universe(args.gro_file, args.xtc_file)
    if args.verbose:
        logging.info("Load universe : " + str(u))
    resid_npa1 = None
    resid_npa2 = None
    resid_arr1 = None
    resid_arr2 = None
    if args.npa_one:
        resid_npa1 = args.npa_one[0].split()
    if args.npa_second:
        resid_npa2 = args.npa_second[0].split()
    if args.arr_one:
        resid_arr1 = args.arr_one[0].split()
    if args.arr_second:
        resid_arr2 = args.arr_second[0].split()
    df_final = create_final_dataframe(resid_arr1, resid_arr2,
                                      resid_npa1, resid_npa2, u)
    if len(output_directory) > 2:
        try:
            os.makedirs(output_directory, exist_ok=True)

            print("Directory '%s' can not be created")
        os.chdir(output_directory)
    if len(output) > 2:
        df_final.to_csv(output, sep="\t", index=False)
    else:
        file_name_tabular = "Calculate_pair_dist_aqp.tabular"
        df_final.to_csv(file_name_tabular, sep="\t", index=False)