old_contents: #!/usr/bin/python
  import sys
  import os
  import inspect
  import subprocess as sub
  import shlex
  
  currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
  parentdir = os.path.dirname(currentdir)
  sys.path.insert(0,parentdir) 
  import common
  import config as cfg
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  def runCommand(cmd, outfile=False):
  	cmd = shlex.split(cmd)
  	
  	if outfile:
  		if os.path.exists(outfile):
  			stdout = open(outfile, 'a')
  			stdout.flush()
  		else:
  			stdout = open(outfile, 'w')
  		p = sub.Popen(cmd, stdout=stdout, stderr=sub.STDOUT)
  		
  	else:
  		p = sub.Popen(cmd)
  		
  	p.wait()
  	
  
  
  
  
  
  
  
  
  
  
  def runOne(fastqFile, mapIdx, trim, statsDir, tempDir, samDir):
    
  	#get environment prepared#
  	mapVars = cfg.Map()
  
   	fastqFile = common.zipping(fastqFile)
  	
  	sampleName = os.path.basename(fastqFile)[:-6]
    
  	statFile = statsDir + sampleName + '.map.stats.txt'
  
    
    
  	#run bowtie#
  	cmd =	mapVars.bowtieOptions +	\
  			[
  			'-5', str(trim[0]), 
  			'-3', str(trim[1]), 
  			mapIdx, 
  			fastqFile, 
  			tempDir + sampleName + '.sam'
  			]
  	cmd = ' '.join(cmd)	
  #	runCommand(cmd, outfile=statFile)
  	
  	
  	
  	#sam to bam#
  	cmd =	[
  			mapVars.samtools, 'view', '-bS', 
  		  	'-o', tempDir + sampleName + '.bam',
  		 	tempDir + sampleName + '.sam'
  			]
  	cmd = ' '.join(cmd)
  #	runCommand(cmd)
  	
  
  	
  	#sort bam#
  	cmd =	[
  			mapVars.samtools, 'sort', 
  		#	'-T', tempDir + sampleName + '.sorted',
  			'-o', tempDir + sampleName + '.sorted.bam',
  		 	tempDir + sampleName + '.bam'
  			]
  	cmd = ' '.join(cmd)
  	print cmd
  	runCommand(cmd)
  	raise SystemExit
  	
  	
  	
  	#remove duplicates#
  	cmd =	[
  			mapVars.samtools, 'rmdup', '-s', 
  			tempDir + sampleName + '.sorted.bam',
  			tempDir + sampleName + '.unique.bam'
  			]
  	cmd = ' '.join(cmd)
  	print cmd
  	runCommand(cmd, outfile=statFile)
  
  	
  	
  	#bam to sam#
  	cmd =	[
  			mapVars.samtools, 'view', '-h', 
  		  	'-o', samDir + sampleName + '.unique.sam',
  		 	tempDir + sampleName + '.unique.bam'
  			]
  	cmd = ' '.join(cmd)
  	print cmd
  	runCommand(cmd)
  
  
  	
  	printText = '\t\tFinished mapping and removing PCR duplicates for ' + os.path.basename(fastqFile)
  	print(printText)
  
  
  
  
  	
  
new_contents: #!/usr/bin/python
  import sys
  import os
  import inspect
  import subprocess as sub
  import shlex
  
  currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
  parentdir = os.path.dirname(currentdir)
  sys.path.insert(0,parentdir) 
  import common
  import config as cfg
  	
  	
  	
  	
  	
  	
  	
  	
  	
  	
  def runCommand(cmd, outfile=False):
  	cmd = shlex.split(cmd)
  	
  	if outfile:
  		if os.path.exists(outfile):
  			stdout = open(outfile, 'a')
  			stdout.flush()
  		else:
  			stdout = open(outfile, 'w')
  		p = sub.Popen(cmd, stdout=stdout, stderr=sub.STDOUT)
  		
  	else:
  		p = sub.Popen(cmd)
  		
  	p.wait()
  	
  
  
  
  
  
  
  
  
  
  
  def runOne(fastqFile, mapIdx, trim, statsDir, tempDir, samDir):
    
  	#get environment prepared#
  	mapVars = cfg.Map()
  
   	fastqFile = common.zipping(fastqFile)
  	
  	sampleName = os.path.basename(fastqFile)[:-6]
    
  	statFile = statsDir + sampleName + '.map.stats.txt'
  
    
    
  	#run bowtie#
  	cmd =	mapVars.bowtieOptions +	\
  			[
  			'-5', str(trim[0]), 
  			'-3', str(trim[1]), 
  			mapIdx, 
  			fastqFile, 
  			tempDir + sampleName + '.sam'
  			]
  	cmd = ' '.join(cmd)	
  #	runCommand(cmd, outfile=statFile)
  	
  	
  	
  	#sam to bam#
  	cmd =	[
  			mapVars.samtools, 'view', '-bS', 
  		  	'-o', tempDir + sampleName + '.bam',
  		 	tempDir + sampleName + '.sam'
  			]
  	cmd = ' '.join(cmd)
  #	runCommand(cmd)
  	
  
  	
  	#sort bam#
  	cmd =	[
  			mapVars.samtools, 'sort', 
  		#	'-T', tempDir + sampleName + '.sorted',
  		#	'-o', tempDir + sampleName + '.sorted.bam',
  		 	tempDir + sampleName + '.bam', 
  			tempDir + sampleName + '.sorted'
  			]
  	
  	cmd = ' '.join(cmd)
  	print cmd
  	runCommand(cmd)
  	raise SystemExit
  	
  	
  	
  	#remove duplicates#
  	cmd =	[
  			mapVars.samtools, 'rmdup', '-s', 
  			tempDir + sampleName + '.sorted.bam',
  			tempDir + sampleName + '.unique.bam'
  			]
  	cmd = ' '.join(cmd)
  	print cmd
  	runCommand(cmd, outfile=statFile)
  
  	
  	
  	#bam to sam#
  	cmd =	[
  			mapVars.samtools, 'view', '-h', 
  		  	'-o', samDir + sampleName + '.unique.sam',
  		 	tempDir + sampleName + '.unique.bam'
  			]
  	cmd = ' '.join(cmd)
  	print cmd
  	runCommand(cmd)
  
  
  	
  	printText = '\t\tFinished mapping and removing PCR duplicates for ' + os.path.basename(fastqFile)
  	print(printText)
  
  
  
  
  	
  
subject: Update mapfile.py