old_contents: #!/usr/bin/python
  
  
  
  
  
  
  
  def trimOne():
  
  
    return 0
  
new_contents: #!/usr/bin/python
  import os
  import gzip
  
  
  
  
  
  
  
  
  
  
  #open input and output files#
  def openFiles(file):
  	
  	if file[-5:] == 'fastq':
  		IN = open(file, 'r')
  		outfilename = file[:-5] + 'k' + str(length) + '.fastq'
  		
  	elif file[-8:] == 'fastq.gz':
  		IN = gzip.open(file, 'rb')
  		outfilename = file[:-8] + 'k' + str(length) + '.fastq'
  		
  	else:
  		errorText = '\nERROR: unrecognized file type to be processing, please ensure only fastq files are being submitted to this pipeline'
  		errorText += '\n\t' + file + '\n'
  		print(errorText)
  		raise SystemExit
  	
  	OUT = open(outfilename, 'w')
  	
  	return IN, OUT
  
  	
  
  	
  	
  	
  	
  	
  	
  	
  #do the trimming (and print out changes)#
  def trimOne(IN, OUT, trim, length):
  	lineCount = 0
  	includeCount = 0
  	includeTest = True
  	for x in IN:
  		lineCount += 1
  		
  		#name line, save information#
  		if (lineCount + 3) % 4 == 0:
  			lines = x
  			
  		#sequence line, test trimming ability#
  		elif (lineCount + 2) % 4 == 0:
  			aline = x.rstrip()
  			if len(aline) >= trim + length:
  				includeTest = True
  				newLine = aline[trim:(trim + length)]
  				lines += newLine + '\n'
  			else:
  				includeTest = False
  				
  		#name line 2, save information#				
  		elif (lineCount + 1) % 4 == 0:
  			lines += x
  			
  		#quality line, write data to file if read is long enough#
  		elif (lineCount) % 4 == 0:
  			if includeTest:
  				newLine = x[trim:(trim + length)]
  				lines += newLine + '\n'
  				OUT.write(lines)
  				includeCount += 1
  			includeTest = True
  			
  	IN.close()
  	OUT.close()
  	
  	printText = '\t\tMaintained ' + str(includeCount) + ' of ' + str(lineCount) + ' fastq reads for ' + file.split('/')[-1] 
  	print(printText)
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  def preprocessOne(file, trim, length, remove=False):
  	IN, OUT = openFiles(file)
  	trimOne(IN, OUT, trim, length)
  	
  	#remove or move full length fastq#
  	if remove:
  		os.remove(file)
  	else:
  		newLoc = os.path.dirname(file) + '/FullLength/' + os.path.basename(file)
  		os.rename(file, newLoc)
  	
  	
  	
  	
  	
  
subject: Update trimfile.py