[英]How to store output from linux call in Python
I am writing a script to sort a file based on a specific column. 我正在编写一个脚本,用于根据特定列对文件进行排序。 I tried calling the 'sort' Linux command for this. 我尝试为此调用“ sort” Linux命令。 The code I am using is: 我使用的代码是:
from subprocess import
path_store = /homes/varshith/maf
input = path_store
field = "-k2"
store_output_in_new_file = ">"
new_path = path_store + "_sort.bed"
sorting = Popen(["sort", field, input, append, new_path], stdout=PIPE)
But this doesn't work properly. 但这不能正常工作。 Thanks in advance for helping. 在此先感谢您的帮助。
Use communicate to get the output: 使用communication获取输出:
from subprocess import PIPE,Popen
sorting = Popen(["sort", field, output, append, new_path], stdout=PIPE)
out, err = sorting.communicate()
print out
Or just use check_output
for python >= 2.7: 或者仅将check_output
用于python> = 2.7:
sorting = check_output(["sort", field, output, append, new_path])
If you want to just write the sorted contents you can redirect stdout to a file object: 如果您只想编写排序的内容,则可以将stdout重定向到文件对象:
output = "path/to/parentfile"
cmd = "sort -k2 {}".format(output)
with open(new_file,"w") as f:
sorting = Popen(cmd.split(),stdout=f)
First of all, I hope that output
and new_path
are actually strings (I assume so, but it's not clear from what you posted). 首先,我希望output
和new_path
实际上是字符串(我假设是这样,但是您发布的内容尚不清楚)。 But assuming all of that is sorted out: 但是,假设所有这些都已解决:
sorting = Popen(...)
sorting_output = sorting.communicate()[0]
That should store the contents of the subprocess's standard output to sorting_output
. 那应该将子流程的标准输出的内容存储到sorting_output
。
To emulate the shell command: 模拟shell命令:
$ sort -k2 /homes/varshith/maf > /homes/varshith/maf_sort.bed
ie, to sort /homes/varshith/maf
file by the 2nd column and to store the sorted output to /homes/varshith/maf_sort.bed
file in Python: 即,按第二列对/homes/varshith/maf
文件进行排序,并将排序后的输出存储到Python中的/homes/varshith/maf_sort.bed
文件中:
#!/usr/bin/env python
from subprocess import check_call
field = '-k2'
input_path = '/homes/varshith/maf'
output_path = input_path + '_sort.bed'
with open(output_path, 'wb', 0) as output_file:
check_call(["sort", field, input_path], stdout=output_file)
It overwrites the output file. 它将覆盖输出文件。 To append to the file instead, use ab
mode instead of wb
. 要附加到文件,请使用ab
模式代替wb
。
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