passing variables from python to bash shell script via os.system

Question

In the following code, I construct a variable $probe1 that I want to then pass to a bash script. I the toy example below, the output is blank, i.e. $probe1 is not recognized the the bash shell script within the os.system call. What needs to be done?

for line1 in datfile:
    datmat=datmat+[line1.rstrip('\n').split('\t')]
        probe=datmat[i][0]
        snp1=datmat[i][2]
    probe1='permprobes'+probe+'pheno.pphe'
    os.system('echo $probe1')

probe1 = '...' sets a Python variable. It has no connection to Bash whatsoever. — Blender
– Blender, Commented Dec 19, 2012 at 1:09
Is there some way to carry over a variable from python to the bash shell? That's essentially my question. — user1815498
– user1815498, Commented Dec 19, 2012 at 1:14
I'm using python to extract some variable names, which I then need to pass as arguments to a program that's executed from a bash script. Therefore, I need to export the string $probe1 to a bash shell (I'm just using echo as a simple example to illustrate the problem) — user1815498
– user1815498, Commented Dec 19, 2012 at 1:22
But why do you need the variables? Why don't you just quote the arguments and pass them directly to the script? — Blender
– Blender, Commented Dec 19, 2012 at 1:23

satoru · Accepted Answer · 2012-12-19 01:14:01Z

10

Seems like this is what you are trying to do:

In [2]: os.environ['probe1'] = 'hello'

In [3]: os.system('echo $probe1')
hello

But I have no idea why you would like to do this ...

answered Dec 19, 2012 at 1:14

satoru

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3 Comments

user1815498 Over a year ago

I'm using python to extract some variable names from a data file, which I then need to pass to a bash shell script to run in another program. The example with echo is just a "toy" script to illustrate the problem of moving a variable from python into a bash shell.

satoru Over a year ago

@user1815498 Maybe you can use a pipe to do that: docs.python.org/2/library/subprocess.html

user1815498 Over a year ago

In any case, the os.environ[ ] solution you propose solves my problem. Thank you for the pipe reference, it will come in handy when I need to pass multiple variables from python to the shell.

jgritty · Accepted Answer · 2012-12-19 01:23:14Z

4

os.system('echo {0}'.format(probe1))

probe1 is a python variable, not a shell variable.

os.environ['probe1'] = probe1

will set the bash environment variable to the python variable contents. Once the python script exits though, the environment variable goes away.

edited Dec 19, 2012 at 1:23

answered Dec 19, 2012 at 1:09

jgritty

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1 Comment

user1815498 Over a year ago

I know that, my question is how I can transfer a python variable to the bash shell.

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