running shelscript inside python

[Albert Hopkins]

On Thu, 2009-03-26 at 15:23 -0700, harijay wrote:
> Hi
> I want to run shell scripts of the following kind from inside python
> and for some reason either the os.system or the subprocess.call ways
> are not working for me .
> 
> I am calling a fortran command (f2mtz ) with some keyworded input that
> is normally piped (<<)  in.
> The section of code that deals with the shell script is as  follows
> 
> script="""HKLIN %s HKLOUT %s <<eof
> SYMM %s
> CELL %s
> format '(3f4.0,f11.2,f8.2,f7.3,4f11.3)'
> skipline 0
> LABOUT H K L IP FOMS PHIS HLA HLB HLC HLD
> CTYPOUT H H H I W P A A A A
> END
> eof
> """ %(options.phs,options.mtzfile,options.symm,cellparams)
> import subprocess
> subprocess.call(["f2mtz" , script])
> 
> Normally I would type the commands above into a shell script and then
> execute it
> for example a file (tmp.sh)
> 
> #!/usr/bin/sh
> f2mtz HKLIN 32_4run1.phs HKLOUT 32_4run1.mtz <<eof
> SYMM p1
> CELL 79.814 102.639 153.627 82.465 75.531 73.450
> format '(3f4.0,f11.2,f8.2,f7.3,4f11.3)'
> skipline 0
> LABOUT H K L IP FOMS PHIS HLA HLB HLC HLD
> CTYPOUT H H H I W P A A A A
> END
> eof
> 
> And then run that script
> "sh tmp.sh"
> 
> 
> When I try subprocess.call(["f2mtz" , script]) or os.system("f2mtz %s"
> % script)
> 

Ask yourself what you are trying to do:

      * Run an executable
      * pass arguments to the executable
      * Use a string standard input to the call

Then re-read over the subprocess module and it should become clearer to
you.