How to make an if loop of a file existence, in python?

Question

I'm trying to run a series of commands for two input files, but I want to avoid doing the same thing if it has already been done. To make it more clear, these are my commands:

from subprocess import call
import os.path

pathway = raw_input("Please give the pathway of your Genome Folder ( .fa files): ")
genome= raw_input("Please type your genome name (e.g. chick_build2.1):" )
#Building a genome (.stidx for stampy)
cmd = "python /space/tierzucht/mgholami/stampy-1.0.13/stampy.py -G %s %s/*.fa" %(genome, pathway)
#Building a genome (.fa for BWA)
cmd = "cat %s/*.fa > %s.fa" %(pathway, genome)
#Building an index (for BWA)
cmd = "bwa index %s.fa " %(genome)
call(cmd, shell=True)

and what I want to do is to add an if loop before each command that if the file already exists do not run this command. I tried this but it doesn't work:

if os.path.isfile("%s.stidx") %genome == False:
  cmd = "python /space/tierzucht/mgholami/stampy-1.0.13/stampy.py -G %s %s/*.fa" %(genome, pathway)

what I'm trying to do is to check if the stidx format of the chosen file name already exists! And I want to do it with fa format and several others too.

Why aren't you using make for this?

Ignacio Vazquez-Abrams
– Ignacio Vazquez-Abrams

2011-11-02 13:41:01 +00:00
Commented Nov 2, 2011 at 13:41 — Ignacio Vazquez-Abrams
– Ignacio Vazquez-Abrams, Commented Nov 2, 2011 at 13:41

NPE · Accepted Answer · 2011-11-02 13:49:09Z

1

Try:

if not os.path.isfile("%s.stidx"%genome):
  cmd = "python /space/tierzucht/mgholami/stampy-1.0.13/stampy.py -G %s %s/*.fa" %(genome, pathway)

In your original code, the paretheses were misplaced (the % was getting interpreted as the remainder operator, so the interpreter did not complain about a syntax error).

edited Nov 2, 2011 at 13:49

answered Nov 2, 2011 at 13:41

NPE

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