calling shell commands from within python

That's quite easy to interact with the shell from within python, it only needs to import the subprocess module.
If the matter is just executing a command, use the call method:

>>>>subprocess.call('ls')
Applications    SharedLin       Volumes         etc             mach_kernel     sbin            var
Developer       SharedXP        bin             home            net             sw
Library         System          cores           iraf            opt             tmp
Network         Users           dev             lost+found      private         usr

If some arguments need to be used, you cannot put them in the same string as the command, need to use:

>>>>subprocess.call(['ls','-l'])
total 40733
drwxrwxr-x+ 134 root                admin      4556 28 jui 00:21 Applications
drwxrwxr-x@  18 root                admin       612 18 mar 20:03 Developer
[...]

or you'll need to execute the command in a shell:
>>>>subprocess.call('ls -l', shell=True)

If one want to deal with the output, use the Popen and communicate methods :

>>>>ls = subprocess.Popen(["ls"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
>>>>stdout, stderr = ls.communicate()
You can access the distinct values of the stdout by splitting them:
stdout.split()

Now, one can need to execute the command with a givenfile as input and redirect the output to another file.
That's possible using the Popen method:

input_file = open('model.in','r')
output_file = open('model.out','wb')
p = subprocess.Popen('cloudy.exe', stdout=output_file, stdin = input_file)
input_file.close()
output_file.close()
That's it!

References:
http://docs.python.org/library/subprocess.html

http://jimmyg.org/blog/2009/working-with-python-subprocess.html