子流程函数python：在自动化中使用

Question

I am trying to run this command in the terminal using Python:

./Pascal --set=settings/1_settings.txt --runpathway=on --genescoring=sum --pval=1_snp_values.txt.gz

I need to run this script 180 times using a different pval everytime. Hence, automating it via Python saves me a lot of time.

Currently I have a Python subprocess like this:

subprocess.call("./Pascal --set=settings/1_settings.txt --runpathway=on --genescoring=sum --pval=1_snp_values.txt.gz")

Although, I am getting this error:

Traceback (most recent call last):
  File "test_automation.py", line 4, in <module>
    subprocess.call("./Pascal --set=settings/1_settings.txt --runpathway=on --genescoring=sum --pval=1_snp_values.txt.gz")
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception

The problem is when I execute the exact same command in terminal (outside of the Python code) it works fine. Am I using the syntax incorrectly?

Answer 1

Using os.system ...

You could try using this to run your terminal command like so:

import os
os.system("./Pascal --set=settings/1_settings.txt --runpathway=on --genescoring=sum --pval=1_snp_values.txt.gz")

And if this works, it is simple to execute in a for-loop to get it to run 180 times:

import os
for _ in range(180):
    os.system("./Pascal --set=settings/1_settings.txt --runpathway=on --genescoring=sum --pval=1_snp_values.txt.gz")

Additionally, if Pascal is in the same directory that you are running your script then the path of ./ is not necessary as by default, it will search the current working directory. So you can change it to just Pascal --set-settings...

Using subprocess.call ...

Personally, I think using os.system is a cleaner solution, however you can use subprocess.call to do the same thing in one of two ways, either:

call Pascal and the other arguments separately from a list like:

import subprocess as s
s.call(['./Pascal', '--set=settings/1_settings.txt', '--runpathway=on', '--genescoring=sum', '--pval=1_snp_values.txt.gz'])

or just set shell to true and pass in the full line as a string like:

import subprocess as s
s.call('./Pascal --set=settings/1_settings.txt --runpathway=on --genescoring=sum --pval=1_snp_values.txt.gz', shell=True)

Hope this works for you!