如何使用python脚本从文本文件中提取数据？
[英]How to extract data from a text file with python script?
问题描述
I have i script in python that should search a data file, and copy the relevant data to separate files. 
我在python中编写了脚本，该脚本应该搜索数据文件，并将相关数据复制到单独的文件中。 Here is the script: 这是脚本：
#!/usr/bin/env python
import os
os.system("grep \"x \" dynamics.out | awk '{print $2}' > coord.dat")
os.system("grep \"Total\" dynamics.out | awk '{print $4}' > total.dat")
os.system("grep \"Kinetic\" dynamics.out | awk '{print $4}' > kinetic.dat")
The problem is that this part that makes the coord.dat file is completely wrong. 问题在于制作coord.dat文件的这一部分是完全错误的。 The output in dynamics.out file is not arranged in such a way that is presumed in this script. dynamics.out文件中的输出未按照此脚本中假定的方式进行排列。 The data file is actually a long series of blocks of data that look like this: 数据文件实际上是一系列长数据块，如下所示：
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
So what I need is from every block of data (there are thousands of them in the file) to get the part that is between the line that says "coordinates" and line that says "velocities". 因此，我需要的是从每个数据块（文件中有成千上万个数据）中获取位于“坐标”行和“速度”行之间的部分。 I need to copy that in one file which would have number 23 (No. of atoms) then an empty line, then this data, then again 23, empty line, data, ... 我需要将其复制到一个文件中，该文件将具有数字23（原子数）然后是一个空行，然后是该数据，然后又是23，空行，数据，...
How do I rewrite the script to do this? 如何重写脚本来做到这一点？ Or can someone please recommend some literature where I can learn this. 或者有人可以推荐一些我可以学到的文献。 I don't know the first thing about Python, but I do have some experience in C and C++ and in Matlab and I understand the basic logic of programming. 我对Python一无所知，但是我在C和C ++以及Matlab上都有一定的经验，并且我了解编程的基本逻辑。 Sorry for the long post, but I thought it would be useful to provide a sample of data. 很抱歉，很长的帖子，但我认为提供数据样本会很有用。 Thank you in advance for any help with this. 在此先感谢您的帮助。
2 个解决方案
解决方案1
0 已采纳 2013-07-23 06:57:38
You could try something like this: 您可以尝试这样的事情：
whole_data = []
grab_lines = False
with open('input','r') as atom_file:
molecule_data = ['23\n\n']
for line in atom_file:
if line.startswith('coordinates'):
grab_lines = True
continue
elif line.startswith('velocities'):
grab_lines = False
if molecule_data:
#just checks that we aren't appending an empty list.
molecule_data.append('\n')
whole_data.append(molecule_data)
molecule_data = ['23\n\n']
if grab_lines: #in python 'is True' is implicit for many types.
molecule_data.append(line)
with open('output','w') as out_file:
for molecule in whole_data:
out_file.write(''.join(molecule))
I copy/pasted your input data a few times, so the contents of my atom_file look like: 我几次复制/粘贴了您的输入数据，所以我的atom_file的内容如下所示：
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
time: 0.2fs
coordinates
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
velocities
0.000241908669 0.000039611121 -0.000250932377
-0.000163805243 -0.000115366290 -0.000017375326
-0.000047784448 0.000248119899 -0.000074616012
0.000272673498 -0.000017362735 0.000399681421
-0.000326634443 -0.000254296236 0.000120448584
-0.000094363714 0.000239927614 -0.000271069374
0.000122625277 0.000053803004 -0.000088144918
-0.000112099948 -0.000143815691 0.000140925518
-0.000020483349 -0.000161160777 0.000050721656
0.000277228119 0.000550968890 -0.000249788972
0.000308946542 0.000944826745 0.000083253008
-0.001453065687 0.000249483273 -0.000194390979
0.000370071103 0.000328142273 -0.000594811431
0.000983242907 -0.000247664001 -0.000337676641
0.000702749595 -0.000531050917 -0.000068247339
-0.000913913436 -0.000822599342 -0.000519543480
0.000657300149 -0.001239306947 0.000033192915
0.000763780031 0.000151892085 -0.000106941733
-0.000111349513 0.000591872099 0.000360147787
0.000283007739 0.000537032161 0.000183614425
-0.001766985000 0.001017499281 -0.000870068723
0.001560592306 -0.000636221326 0.001124910644
-0.000596019125 0.001094375746 0.000048984716
Kinetic energy : 0.030613110934
Electronic energy : -60.105483063648
Total energy : -60.074869952714
Conservation : -0.000000051487
self.forces:
-0.000751933584 -0.004126331042 -0.004033882094
-0.034302855990 0.029127675777 -0.007001211293
0.037731564948 -0.009915059812 0.020878531238
-0.109763802365 -0.102520873021 -0.034608644850
0.033373305433 0.018949006487 -0.015434320612
0.078807110369 0.101440274624 0.031960385836
0.027868883444 -0.012844760956 0.009625682828
0.011817203866 -0.011548503873 0.038027933611
-0.016951256413 -0.005848802217 -0.020755575427
0.002823354740 0.003214778324 -0.005974478408
-0.012101005124 -0.007850077809 0.000381372379
0.001958908572 -0.006446492464 0.003077496955
0.005728700900 -0.005220923285 -0.001710604936
-0.006358072353 -0.016410380723 -0.003938145281
0.000121143012 0.012930928986 -0.005592639661
0.008318475112 0.004530628154 0.009023640965
-0.010548513939 -0.005006070272 0.008756275583
-0.000601535778 -0.003075790288 -0.006209965764
-0.002729816846 -0.003390850759 -0.001421821138
-0.023967939963 0.000603482820 -0.016983439682
-0.006731466272 0.010586445711 -0.001984503303
0.009694983786 0.008555900046 0.002598629870
0.006564564487 0.004265795793 0.001319282998
state for next step: 1
and the contents of my out_file look like: 我的out_file的内容如下所示：
23
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
23
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
23
C 3.952444338331 0.353499658087 0.155475597879
C 2.898759709487 0.271561183058 2.878962426315
C 0.377507660095 1.575527713456 2.766723501812
N -0.435656339866 0.616843403256 0.264424997127
C 1.700335308734 1.369156629701 -1.411382740946
C -2.337147095089 -0.967913098150 -0.045537023463
C -3.526272967903 -1.434075863003 -2.507321890479
C 1.622297308900 0.380583237194 -4.021983342405
O -3.540891745414 -1.784144627448 2.005202557948
H 4.590691590007 -1.467822752968 -0.627674161136
H 5.486618188590 1.704246328926 0.014750183919
H 2.660849255805 -1.743362985878 3.501798747714
H 4.277029595067 1.121286334364 4.194254865266
H 0.568970284045 3.642407977900 2.660909012456
H -1.014510536177 1.242297828699 4.266572018582
H -3.406669591714 0.378282552422 -3.550366695442
H -5.529437662690 -2.075200692969 -2.212384192799
H -2.490387114770 -2.906665564518 -3.579439523150
H 1.675087738572 3.514639806992 -1.458115996333
H -0.116965875674 1.068581149519 -5.163647181683
H 1.470748269634 -1.655673714451 -4.142927345712
H 3.361564138064 1.115048483423 -4.937771405417
H -5.134728946067 -2.640023263298 1.567623789643
edit : you could replace the if grab_lines statement with: 编辑 ：您可以用以下if grab_lines替换if grab_lines语句：
if grab_lines: #in python 'is True' is implicit for many types.
line = [line.split()[0]]+[str(float(element)*.529) for element in line.split()[1:]]+['\n']
molecule_data.append('\t'.join(line))
The middle part of line is called a list comprehension . 中间部分line被称为列表理解 。 If any of this is really unclear just ask. 如果真的不清楚，问一下。
解决方案2
0 2016-02-16 13:53:15
grab_lines = False
with open('input','r') as atom_file:
molecule_data = ['23\n\n']
for line in atom_file:
if line.startswith('coordinates'):
grab_lines = True
continue
elif line.startswith('velocities'):
grab_lines = False
#if molecule_data:
#just checks that we aren't appending an empty list.
#molecule_data.append('\n')
#whole_data.append(molecule_data)
#molecule_data = ['23\n\n']
if grab_lines: #in python 'is True' is implicit for many types.
new_line = molecule_data.append(line)
with open('output','w') as out_file:
for molecule in molecule_data:
out_file.write(molecule)
#out_file.write(''.join(molecule))
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