diff estimate_nb_sub_trajectories.py @ 5:e504457035e5 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/estimate_nb_sub_trajectories.py	Mon May 30 14:21:51 2022 +0000
@@ -0,0 +1,247 @@
+#!/usr/bin/env python3
+
+# coding: utf-8
+"""
+The script allows to estimate the number of sub-trajectories to obtain.
+It also allows to split the trajectory into a number of sub-trajectories.
+# USAGE : estimate_nb_sub_trajectories.py -c : file obtaining with gmx check
+  -log : name of log file (optional) -d : output directory (optional)
+  -o : name of output file (optional)
+  -f : desired number of frames per sub-trajectory (optional)
+  -start : start time of the trajectory (optional)
+  -end : end time of the trajectory (optional)
+"""
+
+__all__ = []
+__author__ = "Agnès-Elisabeth Petit"
+__date__ = "30/05/2022"
+__version__ = "0.8"
+__copyright__ = "(c) 2022 CC-BY-NC-SA"
+
+# Library import
+import argparse
+import logging
+import os
+import sys
+
+import numpy as np
+
+
+def test_setup():
+    global args
+    args = parse_arguments()
+    args.verbose = True
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(
+        description="The script allows to estimate the number of "
+                    "sub-trajectories to obtain. It also allows to split"
+                    " the trajectory into a number of sub-trajectories.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        prefix_chars="-",
+        add_help=True,
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        action="store_true",
+        help="""Information messages to stderr""",
+    )
+    parser.add_argument(
+        "-c",
+        "--input_check",
+        type=str,
+        nargs=1,
+        help=""".txt file obtained with gmx check -f.
+        It contains information about the trajectory""",
+    )
+    parser.add_argument(
+        "-log", "--log_output", type=str,
+        default="log/estimate_nb_sub_trajectories.log",
+        help="""Output for log file. Default :
+        log/estimate_nb_sub_trajectories.log"""
+    )
+    parser.add_argument(
+        "-d", "--output_directory", type=str, nargs=1,
+        default="./",
+        help="""It's output Directory. Default : ./"""
+    )
+    parser.add_argument(
+        "-o",
+        "--output_file",
+        type=str,
+        default="estimated_number_of_sub_trajectories.tsv",
+        help="""Output file. Default : 
+        estimated_number_of_sub_trajectories.tsv""",
+    )
+    parser.add_argument(
+        "-f",
+        "--nb_frames",
+        type=int,
+        default=30,
+        help="""Number of frames per sub-trajectory. Default : 30""",
+    )
+    parser.add_argument(
+        "-start", "--start_traj", type=str,
+        help="""Start of the trajectory to be cut"""
+    )
+    parser.add_argument(
+        "-end", "--end_traj", type=str,
+        help="""End of the trajectory to be cut"""
+    )
+    return parser.parse_args()
+
+
+def search_nbr_steps_time_step(txt_file):
+    """
+    Description : Keeping the number of frames of the complete trajectory and
+     the time between each frame.
+    param txt_file: file obtained with gmx check.
+    return: list that contains the number of frames of the complete trajectory
+     and time between each frame.
+    """
+    if args.verbose:
+        logging.info("\nFunction search_nbr_steps_time_step")
+        logging.info("The input file is " + txt_file)
+    with open(txt_file, "r") as f:
+        len_traj = ""
+        time_step = ""
+        for li in f:
+            li = li.rstrip()
+            if li.startswith("Step"):
+                li2 = li.split()
+                len_traj = int(li2[1])
+                time_step = int(li2[2])
+    if args.verbose:
+        logging.info("The length of the trajectory is " + str(len_traj))
+        logging.info(
+            "The elapsed time between two steps is : " + str(time_step) + " ps"
+        )
+        logging.info("End search_nbr_steps_time_step functions")
+    return len_traj, time_step
+
+
+def estimate_nbr_sub_trajectories(nbr_step_time_step, nbr_frames_traj,
+                                  out_file):
+    """
+    Description: Creation of a tsv file that contains the number of frames
+      of the complete trajectory, the number of sub-trajectories to create,
+      the duration between each frame and the number of frames
+      per sub-trajectory.
+    param nbr_step_time_step: list which contains the number of frames of
+      the complete trajectory and the time between each frame
+    param nbr_frames_traj: number of frames per sub-trajectory
+    param out_file: output file name
+    return: list that contains the number of frames of the complete trajectory,
+      the number of sub-trajectories to create, the duration between
+      each frame and the number of frames per sub-trajectory.
+    output: tsv file
+    """
+    if args.verbose:
+        logging.info("\nFunction estimate_nbr_means")
+        logging.info("The length of the trajectory is " +
+                     str(nbr_step_time_step[0]))
+        logging.info(
+            "The elapsed time between two steps is : "
+            + str(nbr_step_time_step[1])
+            + " ps"
+        )
+        logging.info("The output file is  " + str(out_file))
+    name_columns = [
+        "Length_trajectory (frames)",
+        "Number_sub_trajectories",
+        "Time_steps (ps)",
+        "Number_frames_per_sub_trajectory",
+        "Start_trajectory (frames)",
+        "End_trajectory (frames)",
+    ]
+    time_step = nbr_step_time_step[1]
+    if nbr_step_time_step[2] is not None:
+        start_traj = nbr_step_time_step[2]
+    else:
+        start_traj = 0
+    if nbr_step_time_step[3] is not None:
+        end_traj = nbr_step_time_step[3]
+    else:
+        end_traj = nbr_step_time_step[0] - 1
+    if args.verbose:
+        logging.info(
+            "The first frame of the trajectory is the number "
+            + str(start_traj)
+        )
+        logging.info("The first frame of the trajectory is the number "
+                     + str(end_traj))
+    len_traj = end_traj - start_traj + 1
+    n_sub_traj = len_traj // nbr_frames_traj
+    if args.verbose:
+        logging.info("The estimated number of sub-trajectories is : "
+                     + str(n_sub_traj))
+    list_values = [
+        str(len_traj),
+        str(n_sub_traj),
+        str(time_step),
+        str(nbr_frames_traj),
+        str(start_traj),
+        str(end_traj),
+    ]
+    tab_values = np.asarray([name_columns, list_values])
+    np.savetxt(out_file, tab_values, delimiter="\t", fmt="%s")
+    if args.verbose:
+        logging.info("Save table in the file : " + str(out_file))
+        logging.info("End estimate_nbr_sub_trajectories function")
+
+
+if __name__ == "__main__":
+    args = parse_arguments()
+    if args.output_directory[0].endswith("/"):
+        out_directory = args.output_directory[0]
+    else:
+        out_directory = args.output_directory[0] + "/"
+    if args.verbose:
+        if "/" in args.log_output:
+            log_dir = args.log_output.rsplit("/", 1)[0]
+        else:
+            log_dir = "log/"
+        log_file = args.log_output
+        if not os.path.exists(log_dir):
+            os.makedirs(log_dir)
+        if os.path.isfile(log_file):
+            os.remove(log_file)
+        if args.log_output:
+            logging.basicConfig(
+                filename=log_file,
+                format="%(levelname)s - %(message)s",
+                level=logging.INFO,
+            )
+        else:
+            logging.basicConfig(
+                filename=log_file,
+                format="%(levelname)s - %(message)s",
+                level=logging.INFO,
+            )
+        logging.info("verbose mode on")
+    nb_frames_traj = args.nb_frames
+    if args.start_traj and args.start_traj != "":
+        start_trajectory = int(args.start_traj)
+    else:
+        start_trajectory = None
+    if args.end_traj and args.end_traj != "":
+        end_trajectory = int(args.end_traj)
+    else:
+        end_trajectory = None
+    if args.verbose:
+        logging.info("Start estimate number sub-trajectories")
+    output_file = args.output_file
+    if not args.input_check:
+        print("Please enter the file created with 'gmx_check -f'")
+        if args.verbose:
+            logging.error("Please enter the file created with 'gmx_check -f'")
+        sys.exit(1)
+    nb_steps_time_step = list(search_nbr_steps_time_step(
+        args.input_check[0]))
+    nb_steps_time_step.append(start_trajectory)
+    nb_steps_time_step.append(end_trajectory)
+    output_file = out_directory + output_file
+    estimate_nbr_sub_trajectories(nb_steps_time_step, nb_frames_traj,
+                                  output_file)