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

On Thu, Nov 4, 2010 at 11:37 AM, Matt <macmanes@gmail.com> wrote:
> Hi All,
>
> I am trying to execute a shell script from within python.. =A0This 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: =A0cat file.1 | Fastx_trimmer -n
> COUNT -o file.2
>
> So, =A0know 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 =3D subprocess.call([cat sys.argv[1] | fastx_trimmer -n COUNT -o
> sys.argv[2]], shell=3DTrue)
>

Python is not the shell. Shell commands are not python commands. You
need either a string or a list of strings, so any literal have to be
in quotes. Also, subprocess can't handle the redirection. You need to
run it as two commands.

proc1 =3D subprocess.Popen(["cat", sys.argv[1]],stdout =3D
subprocess.PIPE, shell =3D True)
proc2 =3D subprocess.Popen(["fastx_trimmer", "-n", "COUNT", "-o",
sys.argv[2]],stdin=3Dproc1.stdout, shell=3DTrue)


> 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 =3D subprocess.call([fastx.sh, sys.argv[1], sys.argv[2]],
> shell=3DTrue)
>

Again, you need a string. fastx.sh looks for a python object called
fastx and tries accessing an attribute called sh in that object. Ov
course, there's no such thing. Put quotes around it and it will work.

> 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
>

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

Benjamin Kaplan <benjamin.kaplan@case.edu> wrote:
>
>Python is not the shell. Shell commands are not python commands. You
>need either a string or a list of strings, so any literal have to be
>in quotes. Also, subprocess can't handle the redirection. You need to
>run it as two commands.
>
>proc1 = subprocess.Popen(["cat", sys.argv[1]],stdout =
>subprocess.PIPE, shell = True)
>proc2 = subprocess.Popen(["fastx_trimmer", "-n", "COUNT", "-o",
>sys.argv[2]],stdin=proc1.stdout, shell=True)

I KNOW that we're still working on syntax here, and that it's too early for
optimization, but it bothers me to see "cat" as the first thing in a
pipeline.  You don't actually need two steps here at all:

  proc1 = subprocess.Popen(
      ["fastx_trimmer", "-n", "COUNT", "-o", sys.argv[2],
      stdin=open(sys.argv[1]), shell=True
  )

With this, I don't think you even need "shell=True".
-- 
Tim Roberts, timr@probo.com
Providenza & Boekelheide, Inc.

In message <1vmbd65uaj2snq1v0vo49ktn0lsc2o5m1a@4ax.com>, Tim Roberts wrote:

> I KNOW that we're still working on syntax here, and that it's too early
> for optimization, but it bothers me to see "cat" as the first thing in a
> pipeline.

An anti-UUOC instinct. Very good. :)