Apply 2to3 reduce fixer (not a builtin on Python 3)

$ 2to3 --no-diffs -n -w -f reduce Bio BioSQL Tests Doc Scripts
Skip assorted 2to3 fixers which shouldn't be needed anymore

If new code or changes accidentally break under Python 3,
then hopefully our unit tests will catch that... meanwhile
this should make running 2to3 faster.
Switch do2to3.py to list desired fixers

This makes it easier to see what issues remain for
running all of Biopython as dual Python 2 and 3 code.
Disable assorted 2to3 fixers which we don't need (anymore)

$ 2to3 --no-diffs -n -w -f apply Bio BioSQL Tests Doc Scripts
RefactoringTool: No files need to be modified.

etc
Don't want to use the optional 2to3 idioms fixer

Applying the fixer breaks some of the alignment tests,
align.sort() gives another MSA sorted by record.id,
while sorted(align) tries to return a sorted list of
SeqRecord objects and fails (can't order SeqRecord).
Apply 2to3 ws_comma fixer (white space changes)

$ 2to3 --no-diffs -n -w -f ws_comma Bio BioSQL Tests Doc Scripts
Apply 2to3 ws_comma fixer to doctests in Tutuorial.tex
Apply 2to3 ws_comma fixer to doctests

$ 2to3 --no-diffs -n -w -f ws_comma -d Bio BioSQL Tests Doc Scripts
Disable optional 2to3 set_literal & operator fixers

We're working towards code which works on both
Python 2 and Python 3, so we can't use the new
set literals.

The operator fixer isn't required:

$ 2to3 --no-diffs -n -w -f operator Bio BioSQL Tests Doc Scripts
RefactoringTool: No files need to be modified.
Avoid handle.xreadlines(), iterate over handle

$ 2to3 --no-diffs -n -w -f xreadlines Bio BioSQL Tests Doc Scripts
RefactoringTool: Refactored Bio/SCOP/Raf.py
RefactoringTool: Refactored Scripts/scop_pdb.py
RefactoringTool: Files that were modified:
RefactoringTool: Bio/SCOP/Raf.py
RefactoringTool: Scripts/scop_pdb.py
Don't need to apply 2to3 xreadlines fixer now
Don't need 2to3 funcattrs, ne or standarderror fixers
Selected changes based on the 2to3 filter fixer

I've generally replaced the 2to3 fixer's default dummy
variable of _f with something else.