Remove unnecessary some_dict.keys() calls.

For iteration and membership testing can use the
dictionary directly. This also avoids 2to3 adding
list(...) wrappers as list(some_dict.keys()) in
these cases where is it not needed.

Also fixed some white space and string concatenation.
Fix a typo
Tweaking test_Crystal.py to work on Python 3 unmodified
Tweaking test_SeqRecord.py to work on Python 3 unmodified