用 python提取两个文件之间的内容
本文介绍了用 python提取两个文件之间的内容的处理方法，对大家解决问题具有一定的参考价值，需要的朋友们下面随着小编来一起学习吧！
问题描述
问 题
我有两个文件：
一个文件叫exemple_data.csv 里面包含3个id，每个id一行
ZINC04203483
ZINC26895155
ZINC03651026一个文件叫exemple.sdf里面包含有十个分子，每个分子有id号和它空间结构数据，每个分子以四个"$$$$"作为结尾
ZINC04203483
7 6 0 0 0 0 0 0 0 0999 V2000
1.7848 -1.3593 -0.0709 C 0 0 0 0 0
1.2676 -3.5870 0.7267 C 0 0 0 0 0
1.0097 -2.1011 0.9436 C 0 0 0 0 0
1.6939 -0.0371 -0.0717 N 0 0 0 0 0
2.5202 -2.0619 -0.9208 N 0 0 0 0 0
2.4714 -3.9467 0.8577 O 0 0 0 0 0
0.2468 -4.2712 0.4339 O 0 0 0 0 0
1 4 1 0 0 0
2 6 1 0 0 0
3 1 1 0 0 0
3 2 1 0 0 0
1 5 2 0 0 0
2 7 2 0 0 0
M CHG 2 5 1 6 -1
M END
> <rmsd>
0.238019541
$$$$
ZINC02034713
7 6 0 0 0 0 0 0 0 0999 V2000
1.4359 -3.6052 0.4738 C 0 0 0 0 0
1.9307 -1.1052 0.7490 C 0 0 0 0 0
1.5337 -2.2272 -0.1964 C 0 0 0 0 0
1.5927 0.2012 0.1266 N 0 0 0 0 0
2.4694 -4.0171 1.0694 O 0 0 0 0 0
0.3107 -4.1689 0.3418 O 0 0 0 0 0
2.5239 -2.3360 -1.2177 O 0 0 0 0 0
1 5 1 0 0 0
2 3 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 7 1 0 0 0
1 6 2 0 0 0
M CHG 2 4 1 5 -1
M END
> <rmsd>
0.0787463188
$$$$
ZINC02034711
7 6 0 0 0 0 0 0 0 0999 V2000
1.6225 -3.6225 0.5829 C 0 0 0 0 0
1.0839 -1.1178 0.4821 C 0 0 0 0 0
2.0739 -2.2211 0.1469 C 0 0 0 0 0
1.6545 0.1920 0.0735 N 0 0 0 0 0
0.5089 -4.0191 0.1414 O 0 0 0 0 0
2.4376 -4.2168 1.3471 O 0 0 0 0 0
2.2421 -2.2653 -1.2693 O 0 0 0 0 0
1 5 1 0 0 0
2 3 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 7 1 0 0 0
1 6 2 0 0 0
M CHG 2 4 1 5 -1
M END
> <rmsd>
0.279566735
$$$$
ZINC26895155
8 7 0 0 0 0 0 0 0 0999 V2000
2.1705 -1.5475 -0.5415 C 0 0 0 0 0
1.3387 -3.5612 0.6628 C 0 0 0 0 0
1.3018 -2.0375 0.6037 C 0 0 0 0 0
2.2100 -0.2617 -0.7298 N 0 0 0 0 0
2.8130 -2.5199 -1.2719 N 0 0 0 0 0
2.4811 -4.0619 0.8624 O 0 0 0 0 0
0.2238 -4.1310 0.4963 O 0 0 0 0 0
1.4055 0.3868 0.2119 O 0 0 0 0 0
1 5 1 0 0 0
2 6 1 0 0 0
3 1 1 0 0 0
3 2 1 0 0 0
4 8 1 0 0 0
1 4 2 0 0 0
2 7 2 0 0 0
M CHG 1 6 -1
M END
> <rmsd>
0.274481624
$$$$
ZINC01695856
8 7 0 0 0 0 0 0 0 0999 V2000
1.4057 -3.6199 0.4828 C 0 0 0 0 0
0.6383 -0.9506 1.9111 C 0 0 0 0 0
1.4135 -2.2167 -0.1491 C 0 0 0 0 0
1.6928 -1.0605 0.8132 C 0 0 0 0 0
2.4525 -3.9696 1.0940 O 0 0 0 0 0
0.3286 -4.2614 0.3095 O 0 0 0 0 0
2.4250 -2.2353 -1.1545 O 0 0 0 0 0
1.6953 0.1565 0.0693 O 0 0 0 0 0
1 5 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 4 1 0 0 0
3 7 1 0 0 0
4 8 1 0 0 0
1 6 2 0 0 0
M CHG 1 5 -1
M END
> <rmsd>
0.0781114399
$$$$
ZINC01695854
8 7 0 0 0 0 0 0 0 0999 V2000
1.6021 -3.5832 0.5544 C 0 0 0 0 0
-0.1123 -1.0849 -0.8065 C 0 0 0 0 0
2.0136 -2.1983 0.0239 C 0 0 0 0 0
0.9936 -1.0796 0.2454 C 0 0 0 0 0
0.5225 -4.0604 0.1088 O 0 0 0 0 0
2.4141 -4.0828 1.3866 O 0 0 0 0 0
2.2393 -2.3565 -1.3754 O 0 0 0 0 0
1.6735 0.1723 0.1761 O 0 0 0 0 0
1 5 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 4 1 0 0 0
3 7 1 0 0 0
4 8 1 0 0 0
1 6 2 0 0 0
M CHG 1 5 -1
M END
> <rmsd>
0.284852803
$$$$
ZINC13352867
8 7 0 0 0 0 0 0 0 0999 V2000
1.3740 -3.6291 0.4754 C 0 0 0 0 0
0.5507 -0.9450 1.8830 C 0 0 0 0 0
1.3678 -2.2326 -0.1626 C 0 0 0 0 0
1.6446 -1.1066 0.8351 C 0 0 0 0 0
1.7289 0.1781 0.0725 N 0 0 0 0 0
2.4415 -3.9229 1.0855 O 0 0 0 0 0
0.3299 -4.3189 0.3058 O 0 0 0 0 0
2.4081 -2.2413 -1.1410 O 0 0 0 0 0
1 6 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 4 1 0 0 0
3 8 1 0 0 0
4 5 1 0 0 0
1 7 2 0 0 0
M CHG 2 5 1 6 -1
M END
> <rmsd>
0.0959857255
$$$$
ZINC01695855
8 7 0 0 0 0 0 0 0 0999 V2000
1.6218 -3.6149 0.5878 C 0 0 0 0 0
0.9014 -0.9485 2.0417 C 0 0 0 0 0
2.0724 -2.2038 0.1703 C 0 0 0 0 0
1.1102 -1.0715 0.5348 C 0 0 0 0 0
0.5070 -4.0057 0.1448 O 0 0 0 0 0
2.4420 -4.2214 1.3368 O 0 0 0 0 0
2.2392 -2.2394 -1.2457 O 0 0 0 0 0
1.6552 0.1562 0.0551 O 0 0 0 0 0
1 5 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 4 1 0 0 0
3 7 1 0 0 0
4 8 1 0 0 0
1 6 2 0 0 0
M CHG 1 5 -1
M END
> <rmsd>
0.280759811
$$$$
ZINC03651026
8 7 0 0 0 0 0 0 0 0999 V2000
1.4934 -3.7154 0.5054 C 0 0 0 0 0
2.4732 -1.3603 0.9745 C 0 0 0 0 0
2.6877 0.0369 0.4066 C 0 0 0 0 0
1.7876 -2.3003 -0.0110 C 0 0 0 0 0
2.5054 -4.3269 0.9548 O 0 0 0 0 0
0.2927 -4.0978 0.4363 O 0 0 0 0 0
1.4341 0.6134 0.0639 O 0 0 0 0 0
2.6547 -2.4571 -1.1350 O 0 0 0 0 0
1 5 1 0 0 0
2 3 1 0 0 0
2 4 1 0 0 0
3 7 1 0 0 0
4 1 1 0 0 0
4 8 1 0 0 0
1 6 2 0 0 0
M CHG 1 5 -1
M END
> <rmsd>
0.315417558
$$$$
ZINC13352859
8 7 0 0 0 0 0 0 0 0999 V2000
1.6269 -3.5849 0.5524 C 0 0 0 0 0
-0.0728 -1.1104 -0.9226 C 0 0 0 0 0
2.0361 -2.2127 -0.0019 C 0 0 0 0 0
0.9669 -1.1360 0.1908 C 0 0 0 0 0
1.6474 0.1967 0.2000 N 0 0 0 0 0
0.5319 -4.0279 0.1019 O 0 0 0 0 0
2.4154 -4.0983 1.3946 O 0 0 0 0 0
2.2503 -2.4010 -1.4013 O 0 0 0 0 0
1 6 1 0 0 0
2 4 1 0 0 0
3 1 1 0 0 0
3 4 1 0 0 0
3 8 1 0 0 0
4 5 1 0 0 0
1 7 2 0 0 0
M CHG 2 5 1 6 -1
M END
> <rmsd>
0.302429646
$$$$
我希望通过第一个文件里的3个ID在第二个文件查找相对应的分子信息，然后输入到一个新文件里。或者输入到6个新文件里每个文件包含一个分子的所有信息内容包括"$$$$"结尾。
我自己编了个程序怎么都不成功，有没有神人可以帮我修改或重新写一个
我编的程序可以用python tire_database_sdf.py exemple_data.csv exemple.sdf result.csv
现在的问题是我result里的内容exemple.sdf 一样有十个分子，可我只希望result内容只包含六个分子信息对照exemple_data.csv 里边的3个id。
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import re
filename = sys.argv[1]
inputfile = sys.argv[2]
outfile = sys.argv[3]
def liste_id(filename):
list_id = []
with open(filename,"r") as f:
for i in f:
i = i.strip("\n")
list_id.append(i)
return list_id
identifiant = liste_id(filename)
filout = open(outfile,"w")
with open(inputfile,"r") as filin:
newmol = False
element = []
for line in filin:
for ele in identifiant:
if re.search(ele,line):
newmol = True
if line == "$$$$":
newmol = False
if newmol == True:
filout.write(line)
解决方案
先问个问题：不应该只输出3个分子信息么？怎么会是6个？我看你的ID列表只能对号上3个啊。。
代码有一个地方写错了，python读入文件一行时末尾会带'\n'的，需要先strip掉。
只修改了两行就好了，我都加了注释：
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import re
filename = sys.argv[1]
inputfile = sys.argv[2]
outfile = sys.argv[3]
def liste_id(filename):
list_id = []
with open(filename,"r") as f:
for i in f:
i = i.strip("\n")
list_id.append(i)
return list_id
identifiant = liste_id(filename)
filout = open(outfile,"w")
with open(inputfile,"r") as filin:
newmol = False
element = []
for line in filin:
line = line.strip() # strip '\n' character
for ele in identifiant:
if re.search(ele,line):
newmol = True
if line == "$$$$":
newmol = False
if newmol == True:
filout.write(line + '\n') # append '\n' character输出结果：
ZINC04203483
7 6 0 0 0 0 0 0 0 0999 V2000
1.7848 -1.3593 -0.0709 C 0 0 0 0 0
1.2676 -3.5870 0.7267 C 0 0 0 0 0
1.0097 -2.1011 0.9436 C 0 0 0 0 0
1.6939 -0.0371 -0.0717 N 0 0 0 0 0
2.5202 -2.0619 -0.9208 N 0 0 0 0 0
2.4714 -3.9467 0.8577 O 0 0 0 0 0
0.2468 -4.2712 0.4339 O 0 0 0 0 0
1 4 1 0 0 0
2 6 1 0 0 0
3 1 1 0 0 0
3 2 1 0 0 0
1 5 2 0 0 0
2 7 2 0 0 0
M CHG 2 5 1 6 -1
M END
> <rmsd>
0.238019541
ZINC26895155
8 7 0 0 0 0 0 0 0 0999 V2000
2.1705 -1.5475 -0.5415 C 0 0 0 0 0
1.3387 -3.5612 0.6628 C 0 0 0 0 0
1.3018 -2.0375 0.6037 C 0 0 0 0 0
2.2100 -0.2617 -0.7298 N 0 0 0 0 0
2.8130 -2.5199 -1.2719 N 0 0 0 0 0
2.4811 -4.0619 0.8624 O 0 0 0 0 0
0.2238 -4.1310 0.4963 O 0 0 0 0 0
1.4055 0.3868 0.2119 O 0 0 0 0 0
1 5 1 0 0 0
2 6 1 0 0 0
3 1 1 0 0 0
3 2 1 0 0 0
4 8 1 0 0 0
1 4 2 0 0 0
2 7 2 0 0 0
M CHG 1 6 -1
M END
> <rmsd>
0.274481624
ZINC03651026
8 7 0 0 0 0 0 0 0 0999 V2000
1.4934 -3.7154 0.5054 C 0 0 0 0 0
2.4732 -1.3603 0.9745 C 0 0 0 0 0
2.6877 0.0369 0.4066 C 0 0 0 0 0
1.7876 -2.3003 -0.0110 C 0 0 0 0 0
2.5054 -4.3269 0.9548 O 0 0 0 0 0
0.2927 -4.0978 0.4363 O 0 0 0 0 0
1.4341 0.6134 0.0639 O 0 0 0 0 0
2.6547 -2.4571 -1.1350 O 0 0 0 0 0
1 5 1 0 0 0
2 3 1 0 0 0
2 4 1 0 0 0
3 7 1 0 0 0
4 1 1 0 0 0
4 8 1 0 0 0
1 6 2 0 0 0
M CHG 1 5 -1
M END
> <rmsd>
0.315417558这篇关于用 python提取两个文件之间的内容的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
查看全文
