text: #!/usr/bin/env python3
  """
  Converts the output of CIAlign --help into a config file with the
  default options
  """
  import sys
  
  def main():
  
      infile = sys.argv[1] # python3 CIAlign --help > temp.txt
      outfile = sys.argv[2] # ini file
  
      lines = [line.strip() for line in open(infile).readlines()]
      bigstring = " ".join(lines)
      bigstring = bigstring.split("Required Arguments: ")[1]
      arguments = bigstring.split("--")[1:-1]
      out = open(outfile, "w")
      out.write("# CIAlign Parameters\n")
  
      for argument in arguments:
          nam = argument.split(" ")[0]
          parts = argument.split(" ")[1:]
          if parts[0].upper() == parts[0]:
              parts = parts[1:]
          desc = " ".join(parts)
          desc = desc.replace("  ", " ").strip()
          desc = desc.replace("Optional Arguments:", "").replace(" -h,", "")
          if "Required" not in desc:
              desc, d2 = desc.split("Default: ")
          else:
              desc = desc.replace(" Required", "")
              d2 = "XXXXX"
          if "config" not in desc:
              out.write("# %s\n%s = %s\n" % (desc, nam, d2))
      out.close()
  
  if __name__ == "__main__":
      main()
  