Fix exception class typo
Thank Josha for small fix in Tests/common_BioSQL.py

Raised during https://github.com/biopython/biopython/pull/234
Add comment about cStringIO vs StringIO problem
Tweak test_SeqIO_QualityIO.py to allow cStringIO

Using cStringIO.StringIO("") gives a read only handle.
Using cStringIO.StringIO() gives a writeable handle.

Using StringIO.StringIO("") or StringIO.StringIO() gives
a writeable handle.
Standardise StringIO imports in tests
Fixed another old-style exception
Add some missing copyright & licence statements
Cross-platform and Python 2/3 neutral commands.getoutput in Bio._py3k
Replace commands.getoutput (or subprocess.getoutput) via Bio._py3k

This is a small step towards targetting both Python 2 and 3 without
needing to run 2to3.