[BioPython] how to using python to multiply call a program for caculation

[Leighton Pritchard]

Hi Shulin,

I can't see in your code with the while condition where you are specifying
the residue on the command-line string: the variable 'abc' appears to be
undefined in your code:

calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc

So the above should throw an error.

>From your code, the variable containing the residue number you want to use
in the command line appears to be 'i', and there are a number of ways you
can get your variable 'i' into the command-line string from there,
including:

calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + str(i)
calc = '/home/shulin/program/rescP/resc 1PGA.pdb %d' % i
calc = ' '.join(['/home/shulin/program/rescP/resc 1PGA.pdb', str(i)])


I've not tested the following code, but it may be the sort of thing you're
looking for:

# For this code you only need to import os
import os
# Define the command-line string components once
cmdexe = "/home/shulkin/program/rescP/resc"    # executable location
cmdstructure = "1PGA.pdb"                      # structure for analysis
# Then loop over the residue numbers, building a new command line
# and calling each time
for residue in range(1, 101):
    cmdstr = "%s %s %d > %d.txt" % (cmdexe, cmdstructure, residue, residue)
    #print cmdstr                 # does the command-line look right?
    os.system(cmdstr)             # make the system call
    
Sections of the Python documentation you might find useful here are:

string formatting
http://docs.python.org/lib/typesseq-strings.html

subprocess (which is favoured over os.system):
http://docs.python.org/lib/module-subprocess.html

And you may also be interested in the Python Tutor mailing list:
http://mail.python.org/mailman/listinfo/tutor

I hope this is useful,

L.

On 30/07/2008 01:34, "Shulin Zhuang" <shulin.zhuang at gmail.com> wrote:

> Dear All,
> 
> Here just disturb you a question.
> 
> I make a simple script to execute one program, the script content:
> 
> import string, re, sys, os, time, math
> calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
> os.system(calc)
> 
> I can sucessfully execute this script and get the result file"8.txt.
> 
> 
> In the calc column,  8 is a residue number,  resc is a program. The aim is
> to use resc to calculate residue 8 and get the output 8.txt.
> 
> 
>  I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I use
> above simple script, I should execute 100 times. Therefore, I want to write
> a script to let the python do all the calculations at one time.
> 
> Then I write the script as following:
> 
> import string, re, sys, os, time, math
> i = 1
> while i <=100:
>        calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc
>        i = i +1
> os.system(calc)
> 
> 
> However, when I execute the script and get an error:"The first argument
> should bu numerical"
> 
> Would you like to tell me how to write a good script to tackle this problem.
> great thanks
> 
> Best regards
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405

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