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
dos2unix _ordereddict.py
Sort files for 2to3
Apply bug 19111 fix before call 2to3
Move bug 19111 to just before 2to3 call
Thank Nigel Delaney in NEWS for PhyloXML fix
Remove pointless catch & re-raise
Remove pointless catch & re-raise in TogoWS
Add missing licence headers (specific copyright still needed)
Fix to the English of a section title.
Step 1 in a little SVDSuperimposer reorganisation
Step 2 in a little SVDSuperimposer reorganisation
Step 3, restore SVDSuperimposer module docstring
Step 4, document SVDSuperimposer change in DEPRECATED file
Remove an 'import *' flagged by Eric Talevich
Remove licence duplication, add author copyright line
Apply 2to3 reduce fixer (not a builtin on Python 3)

$ 2to3 --no-diffs -n -w -f reduce Bio BioSQL Tests Doc Scripts