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')

Answer 1

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 ...

Answer 2

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.