Matt wrote: > 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.
You could do it in two steps: >>> from subprocess import * >>> source = Popen(["cat", "/usr/share/dict/words"], stdout=PIPE) >>> call(["wc"], stdin=source.stdout) 98569 98568 931708 0 >>> A similar example is here, under a "can't miss" headline: http://docs.python.org/library/subprocess.html#replacing-shell-pipeline Peter -- http://mail.python.org/mailman/listinfo/python-list
