old_contents: #!/usr/local/bin/python
  '''
  Large integration test script.
  '''
  
  import os, sys, subprocess, filecmp, shutil, shlex
  from optparse import OptionParser
  
  def test_integration(msgsteiner):
  
      parser=OptionParser()  
  
      parser.add_option('--msgsteiner',dest='msgsteiner',type='string',help='Path to msgsteiner9 code, be sure to include!')
  
      phos_weights='Tgfb_phos.txt'
  
      #garnet requires a configuration file that has all the data
      forest_out='tgfb_garnet_forest_output'
      garnet_conf='tgfb_garnet.cfg' #provided config file
      gcmd='python ../scripts/garnet.py --outdir=%s %s'%(forest_out,garnet_conf) #command
  
      #forest requires more inputs
      forest_conf='tgfb_forest.cfg' #provided config file
      edge_file='../data/iref_mitab_miscore_2013_08_12_interactome.txt' #interactome
  
      msgsteinerpath=msgsteiner ##WE NEED MSGSTEINER9 INSTALLED!!!
      
      if msgsteinerpath == None:
  	print 'Please provide path to msgsteiner using --msgsteiner option'
  	assert 0
  	
      forest_out='temp'
      seed = 2
      if not os.path.exists(forest_out): ##FOREST WILL NOT CREATE DIRECTORY FOR YOU, GARNET WILL
  	
  	script_dir = os.path.dirname(__file_)
  	abs_file_path = os.path.join(script_dir, forest_out)
          os.makedirs(abs_file_path)
  
          fcmd='python ../scripts/forest.py --prize=%s --edge=%s --conf=%s  --outpath=%s --msgpath=%s --seed=%s'%(phos_weights, edge_file, forest_conf, forest_out, msgsteinerpath, seed)
          subprocess.call(shlex.split(fcmd), shell=False)	
  
  	results = filecmp.cmpfiles('temp', 'tgfb_forest_output', ['result_augmentedForest.sif', 'result_dummyForest.sif', 'result_edgeattributes.tsv',
  							  'result_info.txt', 'result_nodeattributes.tsv', 'result_optimalForest.sif'], shallow=False)
  	shutil.rmtree('temp')
  	if len(results[0]) != 6:
  		assert 0
  	else:
  		assert 1
  
  
  
  
new_contents: #!/usr/local/bin/python
  '''
  Large integration test script.
  '''
  
  import os, sys, subprocess, filecmp, shutil, shlex
  from optparse import OptionParser
  
  def test_integration(msgsteiner):
  
      parser=OptionParser()  
  
      parser.add_option('--msgsteiner',dest='msgsteiner',type='string',help='Path to msgsteiner9 code, be sure to include!')
  
      phos_weights='Tgfb_phos.txt'
  
      #garnet requires a configuration file that has all the data
      forest_out='tgfb_garnet_forest_output'
      garnet_conf='tgfb_garnet.cfg' #provided config file
      gcmd='python ../scripts/garnet.py --outdir=%s %s'%(forest_out,garnet_conf) #command
  
      #forest requires more inputs
      forest_conf='tgfb_forest.cfg' #provided config file
      edge_file='../data/iref_mitab_miscore_2013_08_12_interactome.txt' #interactome
  
      msgsteinerpath=msgsteiner ##WE NEED MSGSTEINER9 INSTALLED!!!
      
      if msgsteinerpath == None:
          print 'Please provide path to msgsteiner using --msgsteiner option'
          assert 0
  	
      forest_out='temp'
      seed = 2
      if not os.path.exists(forest_out): ##FOREST WILL NOT CREATE DIRECTORY FOR YOU, GARNET WILL
  	
          script_dir = os.path.dirname(__file__)
          abs_file_path = os.path.join(script_dir, forest_out)
          os.makedirs(abs_file_path)
  
          fcmd='python ../scripts/forest.py --prize=%s --edge=%s --conf=%s  --outpath=%s --msgpath=%s --seed=%s'%(phos_weights, edge_file, forest_conf, forest_out, msgsteinerpath, seed)
          subprocess.call(shlex.split(fcmd), shell=False)	
  
          results = filecmp.cmpfiles('temp', 'tgfb_forest_output', ['result_augmentedForest.sif', 'result_dummyForest.sif', 'result_edgeattributes.tsv',
  							  'result_info.txt', 'result_nodeattributes.tsv', 'result_optimalForest.sif'], shallow=False)
          shutil.rmtree('temp')
          if len(results[0]) != 6:
              assert 0
          else:
              assert 1
  
  
  
  
subject: Fix indendation and __file__ typo