A couple of things for ya:
The loading would be "better" like this:
with file('morsecodes.txt', 'rt') as f:
for line in f:
line = line.strip()
if len(line) > 0:
# do your stuff to parse the file
That way you don't need to close, and you don't need to manually load each line, etc., etc.
for letter in userInput:
if ValidateLetter(letter): # you need to define this
code = GetMorseCode(letter) # from my other answer
# do whatever you want