title: subprocess.call() or subprocess.Popen for generating/using output files
body: <p>I am trying to write a Python code to interact with another software that uses command line prompts. Once the command line prompt is executed, multiple output files are generated in the directory and the software uses those output files to do some calculations. Plus, the rest of my program utilizes those output files. Currently, I run my python code, then manually enter in the command line prompt, then call the rest of my code and that works fine, however when I attempted to put: </p>
  
  <pre><code>subprocess.call(['sfit4Layer0.py', '-bv5', '-fs'], shell=False)
  </code></pre>
  
  <p>into my file, it does not execute properly (the output files are not generated). </p>
  
  <p>When I made the above code it's own individual python code and called it immediately after the first part of my code - it also worked.</p>
  
  <p>According to my output, I am convinced that the problem is this: the call generated multiple files and then uses those files to make calculations, however, it is not generating the proper files so I get errors in my output. So in a way it seems like it is getting ahead of itself: not waiting for the output files to be produced before making calculations, but again, it works when I run this command separately outside of the program. Any ideas on why this would happen?</p>
  
  <p>What am I doing wrong? Do I need to specify the directory (could the output files be put somewhere else in my computer)? Do I need to use subprocess.Popen ? I have searched the internet but I am new(ish) to Python and thoroughly stumped.</p>
  
  <p>Any suggestions welcome. Thanks!</p>
  
  <p>EDIT: for those who asked, here is the sfit4Layer0.py code:</p>
  
  <pre><code>#! /usr/bin/python
  ##! /usr/local/python-2.7/bin/python
  ##! /usr/bin/python
  ##! /usr/bin/python
  # Change the above line to point to the location of your python executable
  #----------------------------------------------------------------------------------------
  # Name:
  #        sfit4Layer0.py
  #
  # Purpose:
  #       This file is the zeroth order running of sfit4. It accomplishes the following:
  #           1) Calls pspec to convert binary spectra file (bnr) to ascii (t15asc)
  #           2) Calls hbin to gather line parameters from hitran
  #           3) Calls sfit4
  #           4) Calls error analysis from Layer1mods.py
  #           5) Clean outputs from sfit4 call
  #
  #
  # External Subprocess Calls:
  #           1) pspec executable file from pspec.f90
  #           2) hbin  executable file from hbin.f90
  #           3) sfit4 executable file from sfit4.f90
  #                       4) errAnalysis from Layer1mods.py
  #
  #
  #
  # Notes:
  #   1) Options include:
  #            -i &lt;dir&gt;     : Optional. Data directory. Default is current working directory
  #            -b     &lt;dir/str&gt; : Optional. Binary directory. Default is hard-code.
  #            -f &lt;str&gt;     : Run flags, h = hbin, p = pspec, s = sfit4, e = error analysis, c = clean
  #
  #
  # Usage:
  #       ./sfit4Layer0.py [options]
  #
  #
  # Examples:
  #       1) This example runs hbin, pspec, sfit4, error analys, and cleans working directory prior to execution
  #           ./sfit4Layer0.py -f hpsec
  #
  #       2) This example just runs sfit4
  #           ./sfit4Layer0.py -f s
  #
  #       3) This example cleans the output file created by sfit4 in directory (/User/home/datafiles/) which is not the current directory
  #          ./sfit4Layer0.py -i /User/home/datafiles/ -f c
  #
  # Version History:
  #       Created, May, 2013  Eric Nussbaumer (ebaumer@ucar.edu)
  #
  #
  # License:
  #    Copyright (c) 2013-2014 NDACC/IRWG
  #    This file is part of sfit4.
  #
  #    sfit4 is free software: you can redistribute it and/or modify
  #    it under the terms of the GNU General Public License as published by
  #    the Free Software Foundation, either version 3 of the License, or
  #    any later version.
  #
  #    sfit4 is distributed in the hope that it will be useful,
  #    but WITHOUT ANY WARRANTY; without even the implied warranty of
  #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  #    GNU General Public License for more details.
  #
  #    You should have received a copy of the GNU General Public License
  #    along with sfit4.  If not, see &lt;http://www.gnu.org/licenses/&gt;
  #
  #----------------------------------------------------------------------------------------
  
  
  #---------------
  # Import modules
  #---------------
  import sys
  import os
  import getopt
  import sfitClasses as sc
  from Layer1Mods import errAnalysis
  from Tkinter import Tk
  from tkFileDialog import askopenfilename
  
  
  #------------------------
  # Define helper functions
  #------------------------
  def usage(binDirVer):
          print 'sfit4Layer0.py -f &lt;str&gt; [-i &lt;dir&gt; [-b &lt;dir/str&gt; ] \n'
          print '-i &lt;dir&gt;     Data directory. Optional: default is current working directory'
          print '-f &lt;str&gt;     Run Flags: Necessary: h = hbin, p = pspec, s = sfit4, e = error analysis, c = clean'
          print '-b &lt;dir/str&gt; Binary sfit directory. Optional: default is hard-coded in main(). Also accepts v1, v2, etc.'
          for ver in binDirVer:
                  print '             {}: {}'.format(ver,binDirVer[ver])        
  
          sys.exit()
  
  
  def main(argv):
  
          #----------------
          # Initializations
          #----------------
           #------------
           # Directories
           #------------
          wrkDir    = os.getcwd()                              # Set current directory as the data directory
          binDir    = '/data/bin'                              # Default binary directory. Used of nothing is specified on command line
          binDirVer = {
          'v1':   '/data/ebaumer/Code/sfit-core-code/src/',    # Version 1 for binary directory (Eric)
          'v2':   '/data/tools/400/sfit-core/src/',             # Version 2 for binary directory (Jim)
          'v3':   '/Users/jamesw/FDP/sfit/400/sfit-core/src/',             # Version 2 for binary directory (Jim)
          'v4':   '/home/ebaumer/Code/sfit4/src/',
          'v5':   '/Users/allisondavis/Documents/Summer2016/sfit4_0.9.4.3/src'
          }
  
  
           #----------
           # Run flags
           #----------
          hbinFlg  = False                                          # Flag to run hbin
          pspecFlg = False                                          # Flag to run pspec
          sfitFlg  = False                                          # Flag to run sfit4
          errFlg   = False                                          # Flag to run error analysis
          clnFlg   = False                                          # Flag to clean directory of output files listed in ctl file
  
          #--------------------------------
          # Retrieve command line arguments
          #--------------------------------
          try:
                  opts, args = getopt.getopt(sys.argv[1:], 'i:b:f:?')
  
          except getopt.GetoptError as err:
                  print str(err)
                  usage(binDirVer)
                  sys.exit()
  
          #-----------------------------
          # Parse command line arguments
          #-----------------------------
          for opt, arg in opts:
                  # Data directory
                  if opt == '-i':
                          wrkDir = arg
                          sc.ckDir(wrkDir,exitFlg=True)
  
                  # Binary directory
                  elif opt == '-b':
                          if not sc.ckDir(arg,exitFlg=False,quietFlg=True):
                                  try:             binDir = binDirVer[arg.lower()]
                                  except KeyError: print '{} not a recognized version for -b option'.format(arg); sys.exit()
  
                          else: binDir = arg
  
                          if not(binDir.endswith('/')): binDir = binDir + '/'
  
                  # Run flags
                  elif opt == '-f':
                          flgs = list(arg)
                          for f in flgs:
                                  if   f.lower() == 'h': hbinFlg  = True
                                  elif f.lower() == 'p': pspecFlg = True
                                  elif f.lower() == 's': sfitFlg  = True
                                  elif f.lower() == 'e': errFlg   = True
                                  elif f.lower() == 'c': clnFile  = True
                                  else: print '{} not an option for -f ... ignored'.format(f)
                  elif opt == '-?':
                          usage(binDirVer)
                          sys.exit()                        
  
                  else:
                          print 'Unhandled option: {}'.format(opt)
                          sys.exit()
  
          #--------------------------------------
          # If necessary change working directory
          # to directory with input data.
          #--------------------------------------
          if os.path.abspath(wrkDir) != os.getcwd(): os.chdir(wrkDir)
          if not(wrkDir.endswith('/')): wrkDir = wrkDir + '/'
  
          #--------------------------
          # Initialize sfit ctl class
          #--------------------------
          ctlFileName = wrkDir + 'sfit4.ctl'
          if sc.ckFile(wrkDir+'sfit4.ctl'): ctlFileName = wrkDir + 'sfit4.ctl'
          else:
                  Tk().withdraw()
                  ctlFileName = askopenfilename(initialdir=wrkDir,message='Please select sfit ctl file')
  
          ctlFile = sc.CtlInputFile(ctlFileName)
          ctlFile.getInputs()
  
          #------------------------
          # Initialize sb ctl class
          #------------------------
          if errFlg:
                  if sc.ckFile(wrkDir+'sb.ctl'): sbCtlFileName = wrkDir + 'sb.ctl'
                  else:
                          TK().withdraw()
                          sbCtlFileName = askopenfilename(initialdir=wrkDir,message='Please select sb ctl file')
  
                  sbCtlFile = sc.CtlInputFile(sbCtlFileName)
                  sbCtlFile.getInputs()
  
          #---------------------------
          # Clean up output from sfit4
          #---------------------------
          if clnFlg:
                  for k in ctlFile.inputs['file.out']:
                          if 'file.out' in k:
                                  try:            os.remove(wrkDir + ctlFile.inputs[k])
                                  except OSError: pass
  
          #----------
          # Run pspec
          #----------
          if pspecFlg:
                  print '*************'
                  print 'Running pspec'
                  print '*************'
                  rtn = sc.subProcRun( [binDir + 'pspec'] )
  
          #----------
          # Run hbin
          #----------
          if hbinFlg:
                  print '************'
                  print 'Running hbin'
                  print '************'
                  rtn = sc.subProcRun( [binDir + 'hbin'] )
  
          #----------
          # Run sfit4
          #----------
          if sfitFlg:
                  print '************'
                  print 'Running sfit'
                  print '************'
                  rtn = sc.subProcRun( [binDir + 'sfit4'] )
  
          #-------------------
          # Run error analysis
          #-------------------
          if errFlg:
                  print '**********************'
                  print 'Running error analysis'
                  print '**********************'
                  rtn = errAnalysis(ctlFile,sbCtlFile,wrkDir)
  
  
  
  if __name__ == "__main__":
          main(sys.argv[1:])
  </code></pre>