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I have this notebook:

arg1 = "input.txt";
arg2 = "output.txt";
u1 = Import[arg1, "Table"];
u2 = u1(*extremely complicated and long chain of operations*);
Export[arg2, u2]

and I would like to run it in a Python program like this:

def run(arg1,arg2):

for i in range(100):
    run("input{}".format(i), "output{}".format(i))

How can I do this? Preferably without GUI and several threads in parallel (I can use 4 cores in Mathematica).

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related - if you don't mind putting things into a function: mathematica.stackexchange.com/questions/4643/… –  Jonie Aug 20 '13 at 12:08
Does this also works for code in my notebook which lies at some arbitrary location on my machine? –  Danvil Aug 20 '13 at 12:36

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