text: #!/usr/bin/python
  
  import sys, gzip
  
  if len(sys.argv) < 3:
      print "plink2treemix.py [gzipped input file] [gzipped output file]"
      print "ERROR: improper command line"
      exit(1)
  infile = gzip.open(sys.argv[1])
  outfile = gzip.open(sys.argv[2], "w")
  
  
  pop2rs = dict()
  rss = list()
  rss2 = set()
  
  line = infile.readline()
  line = infile.readline()
  while line:
      line = line.strip().split()
      rs = line[1]
      pop = line[2]
      mc = line[6]
      total = line[7]
      if rs not in rss2: 
          rss.append(rs)
      rss2.add(rs)
      if pop2rs.has_key(pop)==0:
          pop2rs[pop] =  dict()
      if pop2rs[pop].has_key(rs)==0:
          pop2rs[pop][rs] = " ".join([mc, total])
      line = infile.readline()
  
  pops = pop2rs.keys()
  for pop in pops:
      print >> outfile, pop,
  print >> outfile, ""
  
  for rs in rss:
      for pop in pops:
          tmp = pop2rs[pop][rs].split()
          c1 = int(tmp[0])
          c2 = int(tmp[1])
          c3 = c2-c1
          print >> outfile, ",".join([str(c1), str(c3)]),
      print >> outfile, ""
  
  