old_contents: #! /usr/bin/env python
  # Generate site positions in genome from given restriction enzyme
  # Juicer 1.5
  import sys
  import subprocess
  import re
  
  if len(sys.argv) != 3 and len(sys.argv) != 4:
  	print 'Usage: %s <restriction enzyme> <genome> [location]' % (sys.argv[0])
  	sys.exit(1)
  
  if sys.argv[1]=='HindIII':
  	teststring='AAGCTT'
  elif sys.argv[1]=='DpnII':
  	teststring='GATC'
  elif sys.argv[1]=='MboI':
  	teststring='GATC'
  else:
  	print 'Usage: %s <restriction enzyme> <genome> [location]' % (sys.argv[0])
  	print '<restriction enzyme> must be defined in script, such as "HindIII" or "DpnII" '
  	sys.exit(1)
  
  genome=sys.argv[2]
  if genome == 'hg19':
    filename='/seq/references/Homo_sapiens_assembly19.fasta'
  elif genome == 'mm9':
    filename='/seq/references/Mus_musculus_assembly9.fasta'
  elif genome == 'mm10':
    filename='/seq/references/Mus_musculus_assembly10.fasta'
  elif genome == 'hg18':
    filename='/seq/references/Homo_sapiens_assembly18.fasta'
  elif len(sys.argv) == 4:
    filename=sys.argv[3]
  else:
    print 'Usage: %s <restriction enzyme> <genome> [location]' % (sys.argv[0])
    print '<genome> not found and [location] not defined'
    sys.exit(1)
  
  check=[]
  teststring=teststring.lower()
  for i in teststring:
    check.append(i)
  f=open(filename,'r')
  g=open(genome+"_"+sys.argv[1]+'.txt','w')
  chromosomecheck=f.readline()
  while (chromosomecheck):
    if (chromosomecheck.startswith('>')):
      firststr=re.split('\s*',chromosomecheck[1:]);
      g.write(firststr[0])
      g.write(' ')
      next=f.read(len(check))
      next=next.lower()
      list=[]
      for i in next:
        list.append(i)
      counter=1
      while len(next)!=0:
        if list==check:
          counterstring=str(counter)
          g.write(counterstring)
          g.write(' ')
        list.pop(0)
        next=f.read(1)
        next=next.lower()
        if next=='\n':
          next=f.read(1)
          next=next.lower()
        if next=='>':
          break
        list.append(next)
        counter+=1
      counter+=len(check)-1
      counterstring=str(counter)
      g.write(counterstring)
      g.write('\n')
      chromosomecheck=next+f.readline()
    else:
      chromosomecheck=f.readline()
  print chromosomecheck
              
  f.close()
  g.close()
              
  
new_contents: #! /usr/bin/env python
  # Generate site positions in genome from given restriction enzyme
  # Juicer 1.5
  import sys
  import subprocess
  import re
  
  if len(sys.argv) != 3 and len(sys.argv) != 4:
  	print 'Usage: %s <restriction enzyme> <genome> [location]' % (sys.argv[0])
  	sys.exit(1)
  
  if sys.argv[1]=='HindIII':
  	teststring='AAGCTT'
  elif sys.argv[1]=='DpnII':
  	teststring='GATC'
  elif sys.argv[1]=='MboI':
  	teststring='GATC'
  else:
  	print 'Usage: %s <restriction enzyme> <genome> [location]' % (sys.argv[0])
  	print '<restriction enzyme> must be defined in script, such as "HindIII" or "DpnII" '
  	sys.exit(1)
  
  genome=sys.argv[2]
  if len(sys.argv) == 4:
    filename=sys.argv[3]
  elif genome == 'hg19':
    filename='/seq/references/Homo_sapiens_assembly19.fasta'
  elif genome == 'mm9':
    filename='/seq/references/Mus_musculus_assembly9.fasta'
  elif genome == 'mm10':
    filename='/seq/references/Mus_musculus_assembly10.fasta'
  elif genome == 'hg18':
    filename='/seq/references/Homo_sapiens_assembly18.fasta'
  else:
    print 'Usage: %s <restriction enzyme> <genome> [location]' % (sys.argv[0])
    print '<genome> not found and [location] not defined'
    sys.exit(1)
  
  check=[]
  teststring=teststring.lower()
  for i in teststring:
    check.append(i)
  f=open(filename,'r')
  g=open(genome+"_"+sys.argv[1]+'.txt','w')
  chromosomecheck=f.readline()
  while (chromosomecheck):
    if (chromosomecheck.startswith('>')):
      firststr=re.split('\s*',chromosomecheck[1:]);
      g.write(firststr[0])
      g.write(' ')
      next=f.read(len(check))
      next=next.lower()
      list=[]
      for i in next:
        list.append(i)
      counter=1
      while len(next)!=0:
        if list==check:
          counterstring=str(counter)
          g.write(counterstring)
          g.write(' ')
        list.pop(0)
        next=f.read(1)
        next=next.lower()
        if next=='\n':
          next=f.read(1)
          next=next.lower()
        if next=='>':
          break
        list.append(next)
        counter+=1
      counter+=len(check)-1
      counterstring=str(counter)
      g.write(counterstring)
      g.write('\n')
      chromosomecheck=next+f.readline()
    else:
      chromosomecheck=f.readline()
  print chromosomecheck
              
  f.close()
  g.close()
              
  
subject: Fix error filename