comparison cut_trajectory.py @ 8:d45cecb7cfd0 draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"

7:f1dd5d99ea2d

    out_traj = (str(out_dir) + prefix_name_file + "_traj_" + str(k) + ".xtc")
    bash_command = ("echo " + n_group + " | gmx trjconv -f " + xtc_file
                    + " -s " + gro_file + " -b " + str(v.split(",")[0])
                    + " -e " + str(v.split(",")[1]) + " -o " + out_traj)
    if arguments.verbose:
        log_directory = "log/tmp/log/"
        logging_file = (log_directory
                        + logging_file.rsplit("/", 1)[1].split(".")[0]
                        + "_" + str(k) + ".log")
        if not os.path.exists(log_directory):
            os.makedirs(log_directory)
        f_log = open(logging_file, "w")
        subprocess.run(bash_command, shell=True, stdout=f_log, stderr=f_log)
        f_log.close()
        return logging_file
    else:

8:d45cecb7cfd0

    out_traj = (str(out_dir) + prefix_name_file + "_traj_" + str(k) + ".xtc")
    bash_command = ("echo " + n_group + " | gmx trjconv -f " + xtc_file
                    + " -s " + gro_file + " -b " + str(v.split(",")[0])
                    + " -e " + str(v.split(",")[1]) + " -o " + out_traj)
    if arguments.verbose:
        log_directory = "log/tmp/"
        logging_file = (log_directory
                        + logging_file.rsplit("/", 1)[1].split(".")[0]
                        + "_" + str(k) + ".log")
        try:
            os.makedirs(log_directory, exist_ok=True)
        except OSError as error:
            print("Directory '%s' can not be created")
        f_log = open(logging_file, "w")
        subprocess.run(bash_command, shell=True, stdout=f_log, stderr=f_log)
        f_log.close()
        return logging_file
    else: