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I want to run an exe file from python with input and saving the output without printing it, does someone know how can I do it?

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Yes, you can. https://docs.python.org/2/library/subprocess.html#module-subprocess

import subprocess

with open('mylog.txt', 'a') as log, open('myerror.txt', 'a') as error_log:
    process = subprocess.call(['ls', '-l'], stderr=error_log, stdout=log)
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