awsemmd_script/data_read.py at master · luwei0917/awsemmd_script · GitHub

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#!/usr/bin/env python3
# @Author: Wei Lu <weilu>
# @Date:   25-Jan-2017
# @Email:  wl45@rice.edu
# @Last modified by:   weilu
# @Last modified time: 25-Jan-2017
# @Copyright: Free


import os
import sys
import argparse
import platform
from datetime import datetime
import imp
from myPersonalFunctions import *
import glob
import numpy as np
import datetime
import pandas as pd
import re
from small_script.myFunctions import readPMF
from small_script.myFunctions import readPMF_2
# Useful codes
# os.system("awk '{print $NF}' all_wham.dat > e_total")
# tr " " "\n"
# sed 1d
# sort -u -k 3
# sed -e 's/+T//'
parser = argparse.ArgumentParser(description="Analysis code, need run multiple times")

# parser.add_argument("protein", help="the name of protein")
# parser.add_argument("template", help="the name of template file")
parser.add_argument("-t", "--test", help="test ", action="store_true", default=False)
parser.add_argument("-d", "--debug", action="store_true", default=False)
parser.add_argument("-l", "--label")
parser.add_argument("--dimension", type=int, default=2)
parser.add_argument("-m", "--mode", type=int, default=0)
parser.add_argument("--force", type=float, default=1.0)
parser.add_argument("-p", "--patch", type=int, default=1)
parser.add_argument("--commons", type=int, default=0)
parser.add_argument("--nsample", type=int, default=2500)
parser.add_argument("--submode", type=int, default=-1)
args = parser.parse_args()

if(args.debug):
    do = print
    cd = print
else:
    do = os.system
    cd = os.chdir

label = args.label

if(args.test):
    print("hello world")

if args.mode == 0:
    data = readPMF(".")
elif args.mode == 1:
    data = readPMF_2(".")  # read all 1d_dis, 1d_qw and 1d_z
elif args.mode ==3:
    all_pmf_list = []
    simulation_list = ["memb_3_rg_0.1_lipid_1_extended", "memb_3_rg_0.1_lipid_1_topology"]
    for simulation in simulation_list:
        for mode in range(3):
            cd(f"nov_15_all_freeEnergy_calculation_sample_range_mode_{mode}")
            cd(simulation)
            tmp = readPMF_2(".").assign(submode=mode, simulation=simulation)
            all_pmf_list.append(tmp)
            cd("../..")
    data = pd.concat(all_pmf_list).reset_index(drop=True)
elif args.mode ==4:
    all_pmf_list = []
    simulation_list = ["next_gen_native_based_memb_3_rg_0.2_lipid_0.6_extended",
                        "next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended",
                        "next_gen_native_based_memb_3_rg_0.4_lipid_0.6_topology"]
    cd(f"all_freeEnergy_calculation_nov11")
    for simulation in simulation_list:

        cd(simulation)
        tmp = readPMF_2(".").assign(submode="0", simulation=simulation)
        all_pmf_list.append(tmp)
        cd("..")
    data = pd.concat(all_pmf_list).reset_index(drop=True)
# data = readPMF(".")
elif args.mode ==5:
    all_pmf_list = []
    simulation_list = ["new_next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended", "new_next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended_2", "new_next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extendedshort"]
    for simulation in simulation_list:
        for mode in range(3):
            cd(f"nov_18_all_freeEnergy_calculation_sample_range_mode_{mode}")
            cd(simulation)
            tmp = readPMF_2(".").assign(submode=mode, simulation=simulation)
            all_pmf_list.append(tmp)
            cd("../..")
    data = pd.concat(all_pmf_list).reset_index(drop=True)
elif args.mode == 6:
    data = readPMF_2(".", is2d=1)  # read all 2d
if args.mode != 6:
    remove_columns = ['bin']
    data = data.drop(remove_columns, axis=1)


destiny = f"{label}_{datetime.datetime.today().strftime('%d_%h_%H%M%S')}.feather"
print(destiny)
data.to_feather(destiny)
os.system(f"cp {destiny} /Users/weilu/Research/data/pulling/{destiny}")
# destiny = f"/Users/weilu/Research/data/pulling/{datetime.datetime.today().strftime('%d_%h')}_data_{label}.feather"