Refactor GenePop's _FileIterator

This way the file open/close is (typically) in one place.
thread->threading and PEP8
Phylo.draw: fix bug where clade branch colors were not set (always shown black)
Deprecate our next methods, my_iterator.next() --> next(my_iterator)

This was based on running 2to3 -f next, and then manually
adding deprecated alias for the next method under Python 2
to preserve backward compatibility (except for SearchIO
where we are free to break the API like this).

Note this also disables the next fixer in do2to3.py
Update Tutorial, my_iterator.next() --> next(my_iterator)
Already using Python 3 style map here, don't need itertools.imap
Don't need this private _any function.

The builtin any function would also have worked (likely
added to Python after this code was written).
Minor Python 3 sorted tweak
Use unittest.assertEquals etc, not assert statements
No longer need the 2to3 import fixer.

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

$ 2to3 --no-diffs -n -w -f import -d Bio BioSQL Tests Doc Scripts
RefactoringTool: Refactored Bio/Phylo/Applications/_Fasttree.py
RefactoringTool: Refactored BioSQL/BioSeqDatabase.py
RefactoringTool: Files that were modified:
RefactoringTool: Bio/Phylo/Applications/_Fasttree.py
RefactoringTool: BioSQL/BioSeqDatabase.py

These two changes are trivial and not actually helpful for
use of the doctests as examples.
Remove obsolete unused private function in Bio.NMR
Idiom, sorted(my_dict.keys())
Minor style change
Style change for sorting lists in SCOP
Style change for sorting lists in SCOP
Bundling copy of MIT licenced 'six' v1.4.1 by Benjamin Peterson
Use six.move.urllib to reduce 2to3 changes
Don't need the 2to3 urllib fixer anymore.

$ 2to3 --no-diffs -n -w -f urllib BioSQL Tests Doc Scripts
RefactoringTool: No files need to be modified.
Replace 'raw_input' with Python3 style 'input' via Bio._six.moves
Don't need the 2to3 raw_input fixer anymore.

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