Running bash commands from python script in certain directory

Question

I am trying to write a Python script to run recursively a program from bash in multiple directories and save(now just display) output in log file.

The problem is that when I try to run that app from home directory just giving the full path of input files it crashes, so I usually run it directly in directory containing input files. I have tried to do this with os.popen() and pexpect but I think most suitable here will be subprocess.

My code:

import subprocess,
from subprocess import Popen, PIPE 

subprocess.Popen("$fp "+pcr+" "+dat, cwd=path+dirs[0], stdout=PIPE)
print output.stdout.read()

where pcr and dat are the names of input files.

As I try to run it I obtain following error:

Traceback (most recent call last):
File "file_ed.py", line 47, in <module>
subprocess.Popen("$fp "+pcr+" "+dat, cwd=retval, stdout=PIPE)
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
 File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

What could be the cause of this problem and how to fix it?

You are trying to access a file or run a command that doesn't exist. There might not be a command $fp, for instance. See this question for info about using environmental variables with subprocess. — Håken Lid
– Håken Lid, Commented Aug 8, 2015 at 14:12
The best way to run a series of bash commands is by writing a bash script to do it. Your approach is doing it the hard way. — msw
– msw, Commented Aug 8, 2015 at 14:22

betterworld · Accepted Answer · 2015-08-08 14:42:39Z

2

I think your problem is that you want to pass pcr and dat as arguments to the program and you think that the whitespace will do that for you – but Python is not bash. Just use an array and it should work:

subprocess.Popen([fp, pcr, dat], cwd=path+dirs[0], stdout=PIPE)

The reason you got "no such file or directory": Python was looking for a program named "$fp "+pcr+" "+dat, i.e. it assumed that the whitespace (and the dollar sign, unless you meant it as kind of a pseudo-code placeholder) is part of the program name. The error tells you that there is no program with such a name.

However it is hard to guess what you mean because your snippet is incomplete. I don't really know what $fp and pcr and dat mean.

Also have a look at the examples in the documentation of the subprocess module.

edited Aug 8, 2015 at 14:42

answered Aug 8, 2015 at 14:22

betterworld

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2 Comments

Silneus Over a year ago

Sorry for this ambiguous $fp dat and pcr. the last two are as I said strings containing input files for the app I want to run. $fp is symbolic link to the app in bash, but I don't think it will work that way so I changed it to the full path. I have solved it using pexpect: child = pexpect.run('/usr/local/bin/FullProf_Suite/fp2k '+pcr+' '+dat,logfile=sys.stdout,cwd=path+dirs[0])

Silneus Over a year ago

where the' path' and 'dirs[0]' are just string forming the path to my work directory. Thanks for reply!

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