input_data = open('input.txt','r') #this opens the file to read it.
 output_data = open('output.txt','w') #this opens a file to write to.

 userStr= (raw_input('Enter the word to be replaced:')) #this prompts the user for a word
 userReplace =(raw_input('What should I replace all occurences of ' + userStr + ' with?')) #this      prompts the user for the replacement word


 for line in input_data:
    words = line.split()
    if userStr in words:
       output_data.write(line + userReplace)
    else:
       output_data.write(line)

 print 'All occurences of '+userStr+' in input.txt have been replaced by '+userReplace+' in   output.txt' #this tells the user that we have replaced the words they gave us


 input_data.close() #this closes the documents we opened before
 output_data.close()

if userStr in words:
   output_data.write(line + userReplace)  # <-- Right here
else:
   output_data.write(line)

for line in input_data:
   while userStr in line:
      index = line.index(userStr)  # The place where `userStr` occurs in `line`.

      # You need to cut `line` into two parts: the part before `index` and
      # the part after `index`. Remember to consider in the length of `userStr`.

      line = part_before_index + userReplace + part_after_index

   output_data.write(line + 'n')  # You still need to add a newline

output_data.write(userReplace.join(line.split(userStr)))