old_contents: from farm_commands2 import *
  import os
  import sys
  from optparse import OptionParser
  from datetime import date
  import glob
  import operator
  import faiReader
  import math
  import shutil
  import string
  
  def main():
      global OPTIONS
      usage = "usage: %prog [options] b36VCF hg18VCF"
      parser = OptionParser(usage=usage)
      parser.add_option("", "--dry", dest="dry",
                          action='store_true', default=False,
                          help="If provided, nothing actually gets run, just a dry run")
                         
      (OPTIONS, args) = parser.parse_args()
      if len(args) != 2:
          parser.error("incorrect number of arguments")
  
      b36vcf, hg18vcf = args
  
      temp = open("tmp", 'w')
      mitotemp = open("mtmp",'w')
      for line in open(b36vcf):
          length = len(line)
          if length > 2 and line[0] != '#':
              if line[0:2] == 'MT':
                  spline = line.split("\t")
                  spline[0] = "chrM"
                  mitotemp.write("\t".join(spline))
              line = 'chr' + line
          temp.write(line)
      out.close()
      mitotemp.close()
      os.system("cat mtmp tmp > "+hg18vcf+" ; rm mtmp ; rm tmp")
  
  if __name__ == "__main__":
      main()
  
new_contents: from farm_commands2 import *
  import os
  import sys
  from optparse import OptionParser
  from datetime import date
  import glob
  import operator
  import faiReader
  import math
  import shutil
  import string
  
  def main():
      global OPTIONS
      usage = "usage: %prog [options] b36VCF hg18VCF"
      parser = OptionParser(usage=usage)
      parser.add_option("", "--dry", dest="dry",
                          action='store_true', default=False,
                          help="If provided, nothing actually gets run, just a dry run")
                         
      (OPTIONS, args) = parser.parse_args()
      if len(args) != 2:
          parser.error("incorrect number of arguments")
  
      b36vcf, hg18vcf = args
  
      temp = open("tmp", 'w')
      mitotemp = open("mtmp",'w')
      for line in open(b36vcf):
          length = len(line)
          if length > 2 and line[0] != '#':
              if line[0:2] == 'MT':
                  spline = line.split("\t")
                  spline[0] = "chrM"
                  mitotemp.write("\t".join(spline))
              line = 'chr' + line
          temp.write(line)
      temp.close()
      mitotemp.close()
      os.system("cat mtmp tmp > "+hg18vcf+" ; rm mtmp ; rm tmp")
  
  if __name__ == "__main__":
      main()
  
subject: Remove legacy "out"