Mercurial > repos > agpetit > calculate_diameter

annotate estimate_cut_sub_trajectories.py @ 3:b120a98cf623 draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
author agpetit
date Fri, 27 May 2022 07:36:52 +0000
parents c574ada16e76
children
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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1 #!/usr/bin/env python3
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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3 # coding: utf-8
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4 """
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5 The script allows to estimate the number of sub-trajectories to obtain.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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6 It also allows to split the trajectory into a number of sub-trajectories.
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7 # USAGE to estimate number of sub-trajectories :
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8 estimate_cut_sub_trajectories.py -c file obtaining with gmx check
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9 -log name of log file (optional) -d output directory (optional)
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10 -o name of output file (optional)
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11 -f desired number of frames per sub-trajectory (optional)
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12 # USAGE to cut trajectory : estimate_cut_sub_trajectories.py
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13 -s number of desired sub-trajectories -gro .gro file
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14 -xtc .xtc file -log name of log file (optional)
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15 -d output directory (optional) -o name of output file (optional)
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16 -g group for output (optional)
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17 """
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19 __all__ = []
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20 __author__ = "Agnès-Elisabeth Petit"
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21 __date__ = "29/04/2022"
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22 __version__ = "0.8"
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23 __copyright__ = "(c) 2022 CC-BY-NC-SA"
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25 # Library import
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26 import argparse
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27 import logging
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28 import os
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29 import subprocess
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30 import sys
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32 from joblib import Parallel, delayed
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34 import numpy as np
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35
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37 def test_setup():
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38 global args
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39 args = parse_arguments()
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40 args.verbose = True
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41
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42
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43 def parse_arguments():
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44 list_choices = []
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45 [list_choices.append(str(x)) for x in range(17)]
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46 parser = argparse.ArgumentParser(
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47 description="The script allows to estimate the number of "
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48 "sub-trajectories to obtain. It also allows to split"
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49 " the trajectory into a number of sub-trajectories.",
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50 formatter_class=argparse.ArgumentDefaultsHelpFormatter,
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51 prefix_chars="-",
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52 add_help=True,
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53 )
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54 parser.add_argument(
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55 "-v",
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56 "--verbose",
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57 action="store_true",
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58 help="""Information messages to stderr""",
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59 )
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60 parser.add_argument(
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61 "-c",
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62 "--input_check",
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63 type=str,
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64 nargs=1,
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65 help=""".txt file obtained with gmx check -f.
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66 It contains information about the trajectory""",
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67 )
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68 parser.add_argument(
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69 "-s",
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70 "--nbr_sub_traj",
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71 type=str,
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72 nargs=1,
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73 help="""numbers of sub_trajectories""",
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74 )
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75 parser.add_argument(
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76 "-gro", "--gro_file", type=str, nargs=1, help="""My input .gro file"""
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77 )
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78 parser.add_argument(
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79 "-xtc", "--xtc_file", type=str, nargs=1, help="""My input .xtc file"""
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80 )
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81 parser.add_argument(
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82 "-log", "--log_output", type=str, nargs=1,
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83 help="""Output for log file"""
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84 )
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85 parser.add_argument(
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86 "-d", "--output_directory", type=str, nargs=1,
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87 help="""It's output Directory"""
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88 )
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89 parser.add_argument(
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90 "-o",
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91 "--output_file",
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92 type=str,
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93 default="estimated_number_of_sub_trajectories.tsv",
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94 help="""Output file""",
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95 )
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96 parser.add_argument(
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97 "-f",
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98 "--nb_frames",
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99 type=int,
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100 default=30,
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101 help="""Number of frames per sub-trajectory""",
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102 )
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103 parser.add_argument(
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104 "-g",
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105 "--group_output",
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106 type=str,
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107 default="0",
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108 choices=list_choices,
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109 help="""Select group for output. 0 : system, 1: protein, 2: protein-H,
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110 3: C-alpha, 4: Backbone, 5: MainChain, 6: MainChain+Cb,
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111 7: MainChain+H, 8: SideChain, 9: SideChain-H, 10: Prot-Masses,
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112 11: non-Protein, 12: Other, 13: POPC, 14: POT, 15: CLA,
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113 16: TIP3""",
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114 )
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115 parser.add_argument(
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116 "-start", "--start_traj", type=str,
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117 help="""Start of the trajectory to be cut"""
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118 )
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119 parser.add_argument(
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120 "-end", "--end_traj", type=str,
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121 help="""End of the trajectory to be cut"""
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122 )
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123 parser.add_argument(
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124 "-cpus", "--number_cpus", type=int,
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125 help="""Number of cpus"""
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126 )
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127 return parser.parse_args()
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128
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129
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130 def search_nbr_steps_time_step(txt_file):
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131 """
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132 Description : Keeping the number of frames of the complete trajectory and
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133 the time between each frame.
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134 param txt_file: file obtained with gmx check.
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135 return: list that contains the number of frames of the complete trajectory
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136 and time between each frame.
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137 """
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138 if args.verbose:
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139 logging.info("\nFunction search_nbr_steps_time_step")
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140 logging.info("The input file is " + txt_file)
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141 with open(txt_file, "r") as f:
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142 len_traj = ""
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143 time_step = ""
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144 for li in f:
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145 li = li.rstrip()
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146 if li.startswith("Step"):
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147 li2 = li.split()
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148 len_traj = int(li2[1])
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149 time_step = int(li2[2])
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150 if args.verbose:
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151 logging.info("The length of the trajectory is " + str(len_traj))
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152 logging.info(
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153 "The elapsed time between two steps is : " + str(time_step) + " ps"
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154 )
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155 logging.info("End search_nbr_steps_time_step functions")
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156 return len_traj, time_step
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157
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158
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159 def search_nbr_sub_traj(tsv_nb_sub_traj_file):
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160 """
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161 Description: Obtaining the number of frames of the complete trajectory,
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162 the number of sub-trajectories to create, the time between each
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163 frame and the number of frames per sub-trajectory.
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164 param tsv_nb_sub_traj_file: tsv file obtained with the estimation of
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165 the number of sub-trajectories
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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166 return: list that contains the number of images of the complete trajectory,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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167 the number of sub-trajectories to create, the time between each image and
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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168 the number of images per sub-trajectory.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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169 """
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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170 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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171 logging.info("\nFunction search_nbr_sub_traj")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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172 logging.info("The input file is " + tsv_nb_sub_traj_file)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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173 list_number_sub_traj = []
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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174 with open(tsv_nb_sub_traj_file, "r") as f:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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175 for li in f:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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176 li = li.rstrip()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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177 if not li.startswith("Length"):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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178 list_number_sub_traj = li.split()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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179 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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180 logging.info("The length of complete trajectory is "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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181 + list_number_sub_traj[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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182 logging.info(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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183 "The number of sub-trajectories required is "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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184 + list_number_sub_traj[1]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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185 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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186 logging.info(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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187 "The elapsed time between two steps is : "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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188 + list_number_sub_traj[2] + "ps"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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189 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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190 logging.info(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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191 "The number of frames per sub-trajectory is "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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192 + list_number_sub_traj[3]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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193 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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194 logging.info("End search_nbr_sub_traj function")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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195 list_number_sub_traj = [int(v) for v in list_number_sub_traj]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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196 return list_number_sub_traj
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197
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198
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199 def launch_cut_traj(list_file, gro_file, xtc_file, out_dir,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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200 logging_file, n_group, n_cpus):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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201 """
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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202 Description: function that allows to split the trajectory
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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203 into a number of sub-trajectories
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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204 param list_file: list that contains the number of images of the complete
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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205 trajectory, the number of sub-trajectories to create, the time between
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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206 each image and the number of images per sub-trajectory.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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207 param gro_file: .gro file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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208 param xtc_file: .xtc file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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209 param out_dir: output directory
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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210 param logging_file: name of log file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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211 return: None
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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212 output: create a number of sub-trajectories
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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213 """
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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214 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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215 logging.info("\nFunction cut_traj")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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216 logging.info("The length of the trajectory is " + str(list_file[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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217 + " frames")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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218 logging.info(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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219 "The elapsed time between two steps is : " + str(list_file[2])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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220 + " ps"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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221 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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222 logging.info("The number of sub-trajectories required is "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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223 + str(list_file[1]))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
224 logging.info(".gro file is " + gro_file)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
225 logging.info(".xtc file is " + xtc_file)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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226 logging.info("Output directory is " + str(out_dir))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
227 logging.info("The name of .log file is " + logging_file)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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228 logging.info("The number of cpus used is " + str(n_cpus))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
229 if not os.path.exists(out_dir):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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230 os.makedirs(out_dir)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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231 n_sub_traj = list_file[1]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
232 times_step = list_file[2]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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233 nb_frame_sub_traj = list_file[3]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
234 prefix_name_file = os.path.basename(gro_file).rsplit(".", 1)[0]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
235 start = list_file[4]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
236 end = list_file[4] - 1
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
237 dict_sub_traj = {}
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
238 for nb_traj in range(n_sub_traj):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
239 end += nb_frame_sub_traj
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
240 value = str(start * times_step) + "," + str(end * times_step)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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diff changeset
241 dict_sub_traj[nb_traj + 1] = value
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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242 start += nb_frame_sub_traj
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
243 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
244 for k, v in dict_sub_traj.items():
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
245 logging.info("Sub_trajectory " + str(k) + " starts at "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
246 + v.split(",")[0] + " ps and ends at "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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247 + v.split(",")[1] + " ps")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
248 logging.info("Launch gmx trjconv\n")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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249 if args.verbose:
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agpetit
parents:
diff changeset
250 list_log_files = Parallel(n_jobs=n_cpus)(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
251 delayed(cut_traj)(out_dir, prefix_name_file, k, v, n_group,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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252 xtc_file, gro_file, logging_file, args)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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253 for k, v in dict_sub_traj.items())
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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254 log_file_complete = open(logging_file, "a")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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255 for f in list_log_files:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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256 open_f = open(f, "r")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
257 [log_file_complete.write(li) for li in open_f.readlines()]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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258 open_f.close()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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259 os.remove(f)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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260 log_file_complete.close()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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parents:
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261 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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262 logging_file = ""
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
263 Parallel(n_jobs=n_cpus)(delayed(cut_traj)(out_dir, prefix_name_file, k,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
264 v, n_group, xtc_file,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
265 gro_file, logging_file, args)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
266 for k, v in dict_sub_traj.items())
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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267 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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268 logging.info("End cut_traj function")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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269
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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270
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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271 def cut_traj(out_dir, prefix_name_file, k, v, n_group, xtc_file, gro_file,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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272 logging_file, arguments):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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273 out_traj = (str(out_dir) + prefix_name_file + "_traj_" + str(k) + ".xtc")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
274 bash_command = ("echo " + n_group + " | gmx trjconv -f " + xtc_file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
275 + " -s " + gro_file + " -b " + str(v.split(",")[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
276 + " -e " + str(v.split(",")[1]) + " -o " + out_traj)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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277 if arguments.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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278 log_directory = "log/tmp/"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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279 logging_file = (log_directory
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
280 + logging_file.rsplit("/", 1)[1].split(".")[0]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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281 + "_" + str(k) + ".log")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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282 if not os.path.exists(log_directory):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
283 os.makedirs(log_directory)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
284 f_log = open(logging_file, "w")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
285 subprocess.run(bash_command, shell=True, stdout=f_log, stderr=f_log)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
286 f_log.close()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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287 return logging_file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
288 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
289 subprocess.run(bash_command, shell=True)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
290
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
291
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
292 def estimate_nbr_sub_trajectories(nbr_step_time_step, nbr_frames_traj,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
293 out_file):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
294 """
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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295 Description: Creation of a tsv file that contains the number of frames
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
296 of the complete trajectory, the number of sub-trajectories to create,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
297 the duration between each frame and the number of frames
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
298 per sub-trajectory.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
299 param nbr_step_time_step: list which contains the number of frames of
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
300 the complete trajectory and the time between each frame
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
301 param nbr_frames_traj: number of frames per sub-trajectory
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
302 param out_file: output file name
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
303 return: list that contains the number of frames of the complete trajectory,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
304 the number of sub-trajectories to create, the duration between
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
305 each frame and the number of frames per sub-trajectory.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
306 output: tsv file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
307 """
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
308 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
309 logging.info("\nFunction estimate_nbr_means")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
310 logging.info("The length of the trajectory is " +
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
311 str(nbr_step_time_step[0]))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
312 logging.info(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
313 "The elapsed time between two steps is : "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
314 + str(nbr_step_time_step[1])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
315 + " ps"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
316 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
317 logging.info("The output file is " + str(out_file))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
318 name_columns = [
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
319 "Length_trajectory (frames)",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
320 "Number_sub_trajectories",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
321 "Time_steps (ps)",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
322 "Number_frames_per_sub_trajectory",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
323 "Start_trajectory (frames)",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
324 "End_trajectory (frames)",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
325 ]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
326 time_step = nbr_step_time_step[1]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
327 if nbr_step_time_step[2] is not None:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
328 start_traj = nbr_step_time_step[2]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
329 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
330 start_traj = 0
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
331 if nbr_step_time_step[3] is not None:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
332 end_traj = nbr_step_time_step[3]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
333 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
334 end_traj = nbr_step_time_step[0] - 1
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
335 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
336 logging.info(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
337 "The first frame of the trajectory is the number "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
338 + str(start_traj)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
339 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
340 logging.info("The first frame of the trajectory is the number "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
341 + str(end_traj))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
342 len_traj = end_traj - start_traj + 1
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
343 n_sub_traj = len_traj // nbr_frames_traj
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
344 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
345 logging.info("The estimated number of sub-trajectories is : "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
346 + str(n_sub_traj))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
347 list_values = [
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
348 str(len_traj),
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
349 str(n_sub_traj),
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
350 str(time_step),
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
351 str(nbr_frames_traj),
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
352 str(start_traj),
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
353 str(end_traj),
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
354 ]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
355 tab_values = np.asarray([name_columns, list_values])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
356 np.savetxt(out_file, tab_values, delimiter="\t", fmt="%s")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
357 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
358 logging.info("Save table in the file : " + str(out_file))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
359 logging.info("End estimate_nbr_sub_trajectories function")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
360
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
361
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
362 if __name__ == "__main__":
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
363 args = parse_arguments()
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
364 if args.output_directory:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
365 if args.output_directory[0].endswith("/"):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
366 out_directory = args.output_directory[0]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
367 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
368 out_directory = args.output_directory[0] + "/"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
369 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
370 out_directory = "./"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
371 if args.log_output:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
372 log_dir = args.log_output[0].rsplit("/", 1)[0]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
373 log_file = args.log_output[0]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
374 if not os.path.exists(log_dir):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
375 os.makedirs(log_dir)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
376 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
377 log_file = "estimate_nb_sub_trajectories.log"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
378 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
379 if os.path.isfile(log_file):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
380 os.remove(log_file)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
381 if args.log_output:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
382 logging.basicConfig(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
383 filename=log_file,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
384 format="%(levelname)s - %(message)s",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
385 level=logging.INFO,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
386 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
387 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
388 logging.basicConfig(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
389 filename=log_file,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
390 format="%(levelname)s - %(message)s",
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
391 level=logging.INFO,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
392 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
393 logging.info("verbose mode on")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
394 nb_frames_traj = args.nb_frames
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
395 gro = ""
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
396 xtc = ""
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
397 if args.nbr_sub_traj:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
398 list_nbr_sub_traj = []
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
399 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
400 logging.info("Cut trajectory mode")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
401 if args.gro_file and ".gro" in args.gro_file[0]:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
402 gro = os.path.basename(args.gro_file[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
403 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
404 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
405 logging.error("The entry is not a file or is not a .gro file")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
406 sys.exit(1)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
407 if args.xtc_file and ".xtc" in args.xtc_file[0]:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
408 xtc = os.path.basename(args.xtc_file[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
409 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
410 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
411 logging.error("The entry is not a file or is not a .xtc file")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
412 sys.exit(1)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
413 if ".tsv" in args.nbr_sub_traj[0]:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
414 list_nbr_sub_traj = search_nbr_sub_traj(args.nbr_sub_traj[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
415 nb_sub_traj = list_nbr_sub_traj[1]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
416 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
417 nb_sub_traj = int(args.nbr_sub_traj[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
418 nb_steps_time_step = search_nbr_steps_time_step(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
419 args.input_check[0])
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
420 if args.start_traj and args.start_traj != "":
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
421 start_trajectory = int(args.start_traj)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
422 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
423 start_trajectory = 0
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
424 if args.end_traj and args.end_traj != "":
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
425 end_trajectory = int(args.end_traj)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
426 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
427 end_trajectory = nb_steps_time_step[0] - 1
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
428 len_trajectory = end_trajectory - start_trajectory + 1
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
429 list_nbr_sub_traj = [
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
430 len_trajectory,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
431 nb_sub_traj,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
432 nb_steps_time_step[1],
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
433 len_trajectory // nb_sub_traj,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
434 start_trajectory,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
435 end_trajectory,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
436 ]
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
437 if nb_sub_traj >= (int(list_nbr_sub_traj[0]) // 2):
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
438 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
439 logging.error(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
440 "The number of averages requested is greater than "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
441 "half the trajectory size"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
442 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
443 print(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
444 "Number of requested sub-trajectories too large compared "
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
445 "to the size of the trajectory"
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
446 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
447 sys.exit(2)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
448 if args.number_cpus:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
449 nb_cpus = args.number_cpus
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
450 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
451 nb_cpus = 2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
452 launch_cut_traj(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
453 list_nbr_sub_traj, gro, xtc, out_directory, log_file,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
454 args.group_output, nb_cpus
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
455 )
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
456 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
457 if args.start_traj and args.start_traj != "":
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
458 start_trajectory = int(args.start_traj)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
459 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
460 start_trajectory = None
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
461 if args.end_traj and args.end_traj != "":
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
462 end_trajectory = int(args.end_traj)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
463 else:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
464 end_trajectory = None
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
465 if args.verbose:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
466 logging.info("Estimate number sub_trajectories mode")
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
467 output_file = args.output_file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
468 nb_steps_time_step = list(search_nbr_steps_time_step(
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
469 args.input_check[0]))
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
470 nb_steps_time_step.append(start_trajectory)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
471 nb_steps_time_step.append(end_trajectory)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
472 output_file = out_directory + output_file
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
473 estimate_nbr_sub_trajectories(nb_steps_time_step, nb_frames_traj,
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
474 output_file)