execute shell script from python, needs sys.argv

Matt macmanes at gmail.com
Thu Nov 4 16:37:27 CET 2010

Hi All,

I am trying to execute a shell script from within python..  This shell
script takes the format, where $1 and $2 are variables from the
command line: cat $1 | Fastx_trimmer -n COUNT -o $2

straight into the cmd line it would be:  cat file.1 | Fastx_trimmer -n
COUNT -o file.2

So,  know that there is a way to do this in python using the
subprocess module, but despite a lot of effort, I can't seem to get
this to work, and precisely because of those arguments taken from the
command line.

I was thinking that the easiest thing to so was to

import sys, os, subprocess
proc = subprocess.call([cat sys.argv[1] | fastx_trimmer -n COUNT -o
sys.argv[2]], shell=True)

this clearly does not work...

alternatively, I could put the shell command in its own file, say
fastx.sh, and pass it's arguments to it vie the command line.

import sys, os, subprocess
proc = subprocess.call([fastx.sh, sys.argv[1], sys.argv[2]],

But, this does not seem to work as this is not the proper way to pass
arguments to the shell script.

in short, I'm sure that this is a easy fix, but given my still limited
python vocabulary, it eludes me.

Thanks, Matt

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