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]], shell=True) 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 -- http://mail.python.org/mailman/listinfo/python-list
