old_contents: #!/usr/bin/python
  import os
  
  from preprocess import trimfile
  import common 
  
  
  
  
  
  
  
  
  
  
  def runAll(args):
  	
  	print('\n\n\nYou have requested preprocess (trim) fastq files')
  	print('\tWARNING:')
  	print('\t\tIF USING ANY LENGTH OTHER THAN 36 BP, REFERENCE FILES ARE NOT SUPPORTED FOR DOWNSTREAM PROCESSING')
  	print('\n')
  	
  
  	#make sure environment is properly prepared#
  	args.FastqDirectory = common.fixDirName(args.FastqDirectory)
  	if not args.remove:
  		common.makeDir(args.FastqDirectory + '/FullLength/')
  
  	
  		
  	#get list of fastq files to process (depending on args.samples)
  	fastqFiles = common.getSampleList(args.FastqDirectory, args.samples, 'fastq')
  	
  	
  	
  	#use the daemon to and preprocessing code to trim all fastq files with parallel processing
  		
  	if args.remove:
  		argList = [(x, args.trim5, args.length, remove=True,) for x in fastqFiles]
  	else:
  		argList = [(x, args.trim5, args.length,) for x in fastqFiles]
  		
  	common.daemon(trimfile.preprocessOne, argList, 'trim sequencing reads to desired length', cpuPerProcess=1)
  		
  	
  	
  	print('\nPre-processing complete\n\n\n')
  
  
new_contents: #!/usr/bin/python
  import os
  
  from preprocess import trimfile
  import common 
  
  
  
  
  
  
  
  
  
  
  def runAll(args):
  	
  	print('\n\n\nYou have requested preprocess (trim) fastq files')
  	print('\tWARNING:')
  	print('\t\tIF USING ANY LENGTH OTHER THAN 36 BP, REFERENCE FILES ARE NOT SUPPORTED FOR DOWNSTREAM PROCESSING')
  	print('\n')
  	
  
  	#make sure environment is properly prepared#
  	args.FastqDirectory = common.fixDirName(args.FastqDirectory)
  	if not args.remove:
  		common.makeDir(args.FastqDirectory + '/FullLength/')
  
  	print args.FastqDirectory
  	
  		
  	#get list of fastq files to process (depending on args.samples)
  	fastqFiles = common.getSampleList(args.FastqDirectory, args.samples, 'fastq')
  	
  	print fastqFiles
  	raise SystemExit
  	
  	
  	#use the daemon to and preprocessing code to trim all fastq files with parallel processing
  		
  	if args.remove:
  		argList = [(x, args.trim5, args.length, remove=True,) for x in fastqFiles]
  	else:
  		argList = [(x, args.trim5, args.length,) for x in fastqFiles]
  		
  	common.daemon(trimfile.preprocessOne, argList, 'trim sequencing reads to desired length', cpuPerProcess=1)
  		
  	
  	
  	print('\nPre-processing complete\n\n\n')
  
  
subject: Update runpreprocess.py