Applied 2to3 -f exec -f execfile

$ 2to3 --no-diffs -n -w -f exec -f execfile Bio BioSQL Tests Doc Scripts
Avoid long literals

$ 2to3 --no-diffs -n -w -f numliterals Bio BioSQL Tests Doc Scripts
Remove unused import
Iteration over a dict uses the keys
Using print function; NOTE - missing expected output file
Correct exception style in this new test
Use our py3k compatible getoutput in this new test
Fixed another print function
Tweak this instance check for nicer post-2to3 result
Fix a few more stray print statements

Aim here is to minimise the differences from running 2to3
to facilitate moving to a single code-base without needing
to run 2to3 at all.