old_contents: #!/usr/bin/python
  import os
  import shutil
  
  from map import mapfile
  import common
  
  
  
  
  
  
  
  
  
  
  def runAll(args):
  	
  	print('\n\n\nYou have requested to map fastq files')
  	print('\tWARNING:')
  	print('\t\tIF USING ANY REFERENCES OTHER THAN THOSE I PROVIDE I CANNOT GUARANTEE RESULT ACCURACY')
  	print('\n')
  
  	
  	
  	#set up environment#
  	args.FastqDirectory = common.fixDirName(args.FastqDirectory)
  	
  	samDir = os.path.dirname(args.FastqDirectory[:-1]) + '/Sam/'
  	if args.output:
  		samDir = common.fixDirName(args.output)
  	
  	statsDir = os.path.dirname(args.FastqDirectory[:-1]) + '/PipelineStats/'
  	if args.statdir:
  		statsDir = common.fixDirName(args.statdir)
  
  	tempDir = args.FastqDirectory + 'Temp/'
  
  	for i in [samDir, tempDir, statsDir]:
  		common.makeDir(i)		
  
  	fastqFiles = common.getSampleList(args.FastqDirectory, args.samples, 'fastq')
  	
  	
  
  	#run multiprocessing of all mapping commands#
  	argList = [(x, args.species, args.trim, statsDir, tempDir, samDir) for x in fastqFiles]
  		
  	common.daemon(mapfile.runOne, argList, 'map fastq files', cpuPerProcess=8)
  
  
  	
  	#remove all temporary files#
  	shutil.rmtree(tempDir[:-1])
    
    
  	
    	print('\nMapping complete\n\n\n')
  
  	
  	
  	
  	
  	
  	
  	
  	
  	
  
new_contents: #!/usr/bin/python
  import os
  import shutil
  
  from map import mapfile
  import common
  
  
  
  
  
  
  
  
  
  
  def runAll(args):
  	
  	print('\n\n\nYou have requested to map fastq files')
  	print('\tWARNING:')
  	print('\t\tIF USING ANY REFERENCES OTHER THAN THOSE I PROVIDE I CANNOT GUARANTEE RESULT ACCURACY')
  	print('\n')
  
  	
  	
  	#set up environment#
  	args.FastqDirectory = common.fixDirName(args.FastqDirectory)
  	
  	samDir = os.path.dirname(args.FastqDirectory[:-1]) + '/Sam/'
  	if args.output:
  		samDir = common.fixDirName(args.output)
  	
  	statsDir = os.path.dirname(args.FastqDirectory[:-1]) + '/PipelineStats/'
  	if args.statdir:
  		statsDir = common.fixDirName(args.statdir)
  
  	tempDir = args.FastqDirectory + 'Temp/'
  
  	for i in [samDir, tempDir, statsDir]:
  		common.makeDir(i)		
  
  	fastqFiles = common.getSampleList(args.FastqDirectory, args.samples, 'fastq')
  	
  	
  
  	#run multiprocessing of all mapping commands#
  	argList = [(x, args.species, args.trim, statsDir, tempDir, samDir) for x in fastqFiles]
  	mapfile.runOne(x, args.species, args.trim, statsDir, tempDir, samDir)
  #	common.daemon(mapfile.runOne, argList, 'map fastq files', cpuPerProcess=8)
  
  
  	
  	#remove all temporary files#
  #	shutil.rmtree(tempDir[:-1])
    
    
  	
    	print('\nMapping complete\n\n\n')
  
  	
  	
  	
  	
  	
  	
  	
  	
  	
  
subject: Update runmap.py