I think

  def sanitize_characters(raw, clean):    
      for line in input_file:
          out = line
          output_file.write(line)
  sanitize_characters(input_file, output_file)

should be

  def sanitize_characters(raw, clean):    
      for line in raw:
          out = line
          clean.write(line)
  sanitize_characters(input_file, output_file)

in your notebook: https://github.com/hundredblocks/concrete_NLP_tutorial/blob/...

Or am I mistaken?