Python 在运行可执行命令之后将输出存储为变量

Question

“TMalign...”是我用来获取数据的可执行文件。我怎样才能将输出存储到一个变量中，以便我可以从输出中提取目标值。可执行文件是从一个很长的 .cpp 编译而来的，所以我不认为我可以从那里调用变量名。

import sys,os
os.system("./TMalign 3w4u.pdb 6bb5.pdb -u 139") #some command I have

输出是这样的，我需要提取 TM-score 值:

*********************************************************************
 * TM-align (Version 20190822): protein structure alignment          *
 * References: Y Zhang, J Skolnick. Nucl Acids Res 33, 2302-9 (2005) *
 * Please email comments and suggestions to yangzhanglab@umich.edu   *
 *********************************************************************

Name of Chain_1: 3w4u.pdb (to be superimposed onto Chain_2)
Name of Chain_2: 6bb5.pdb
Length of Chain_1: 141 residues
Length of Chain_2: 139 residues

Aligned length= 139, RMSD=   1.07, Seq_ID=n_identical/n_aligned= 0.590
TM-score= 0.94726 (if normalized by length of Chain_1, i.e., LN=141, d0=4.42)
TM-score= 0.96044 (if normalized by length of Chain_2, i.e., LN=139, d0=4.38)
TM-score= 0.96044 (if normalized by user-specified LN=139.00 and d0=4.38)
(You should use TM-score normalized by length of the reference structure)

(":" denotes residue pairs of d <  5.0 Angstrom, "." denotes other aligned residues)
SLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSAQLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARFPADFTAEAHAAWDKFLSVVSSVLTEKYR
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::. .
-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK-Y

Total CPU time is  0.03 seconds

感谢您的帮助！

Answer 1

你应该看看下面的方法：

import re
from subprocess import check_output

ret = check_output(['./TMalign', '3w4u.pdb', '6bb5.pdb', '-u', '139'])

tm_scores = []

for line in str(ret).split('\n'):
    if re.match(r'^TM-score=', line):
        score = line.split()[1:2] # Extract the value
        tm_scores.extend(score) # Saving only values

 # tm_scores now contains: ['0.94726', '0.96044', '0.96044']

虽然有些复杂，但它是一个灵活且可调的解决方案。注意，如果要在其他代码中使用，最好把它包装成一个函数。

Answer 2

我的功能不是那么聪明，我会让输出写入一个文件来做下面的事情

import os
cmd = './TMalign 3w4u.pdb 6bb5.pdb -u 139'
os.system(cmd + ">> 1.txt")

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