Fix errors and reformat ptb2ud.py

[alistairewj]

Sometimes ptb2ud.py would raise the following error:

Traceback (most recent call last):
  File "NegBio/negbio/pipeline/ptb2ud.py", line 109, in convert_doc
    self.add_lemmas)
  File "NegBio/negbio/pipeline/ptb2ud.py", line 183, in convert_dg
    ann = annotations[annotation_id_map[node.index]]
IndexError: list index out of range

Fairly sure this was due to self.add_lemmas being interpreted as an annotation offset in the new code, which I've fixed in this PR. I also took the opportunity to change the try/except to not continue the loop on keyboard interrupt.