Guide to using python for bash-style scripting

[4zumanga]

I have a bunch of really horrible hacked-up bash scripts which I would
really like to convert to python, so I can extend and neaten them.
However, I'm having some trouble mapping some constructs easily, and
was wondering if anyone know of a guide to mapping simple uses of
command line programs to python.

For an example, the kind of thing I am thinking of are things like
(yes, this is horrible code).

# These are a run of a program I have written
./proggy -test1  out1
./proggy -test2  out2

#Do some simple manipulation of the output.
grep Node out1  new_out1
grep Node out2  new_out2
diff out1 out2

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Re: Guide to using python for bash-style scripting

[4zumanga]

Yes, there is a stupid mistake in that script, last line should be:

diff new_out1 new_out2

However, this is hopefully not important, what is important is the
general kind of (very simple) things I'm trying to do.

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Re: Guide to using python for bash-style scripting

[Bill Pursell]

4zumanga wrote:
 Yes, there is a stupid mistake in that script, last line should be:

 diff new_out1 new_out2

 However, this is hopefully not important, what is important is the
 general kind of (very simple) things I'm trying to do.

I have been hoping for a good solution to this.  An
easy way to handle simple commands is:

#!/usr/bin/env python

import os
s = echo foo |  sed 's/foo/gap/'  file\n
s += wc -c file\n
s += cat file\n

print s, ***
os.system(s)
 end

(Apologies for the lameness of the commands above).
However, I have some bash scripts that rely on
things like PIPESTATUS, and I have no idea
how to emulate that behavior easily.  How can one
most easily emulate a simple pipe as readily
as in bash?  I've seen a few recipes for doing something
like that, but I haven't yet seen one that i really
like.  Is it possible to execute:
os.system(  a | b | c | d | e)
and retrieve the value of PIPESTATUS?

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Re: Guide to using python for bash-style scripting

[Szabolcs Nagy]

python subprocess module docs:

http://docs.python.org/dev/lib/node517.html

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Re: Guide to using python for bash-style scripting

[James Stroud]

4zumanga wrote:
 I have a bunch of really horrible hacked-up bash scripts which I would
 really like to convert to python, so I can extend and neaten them.
 However, I'm having some trouble mapping some constructs easily, and
 was wondering if anyone know of a guide to mapping simple uses of
 command line programs to python.
 
 For an example, the kind of thing I am thinking of are things like
 (yes, this is horrible code).
 
 # These are a run of a program I have written
 ./proggy -test1  out1
 ./proggy -test2  out2
 
 #Do some simple manipulation of the output.
 grep Node out1  new_out1
 grep Node out2  new_out2
 diff out1 out2
 

Chapter 2 of Mark Lutz's Programming Python (2nd Edition) will make 
you adept at using Python as a (***VASTLY SUPERIOR***) alternative to 
shell scripting. Chapters 3-5 will get you pretty close to master level 
at shell/system scripting.

Note: This is not an intro to python. You should already be able to do 
simple programming in python for Lutz's book to be useful.

James

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James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095

http://www.jamesstroud.com/
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