Mark Tests/SubsMat/acc_rep_mat.pik as binary to solve Pickle problem

If the pickle file has DOS/Windows newlines which can happen under
Windows depending on how git was configured, the C based pickle code
in Python 3.4 fails to to load it with this exception:

_pickle.UnpicklingError: the STRING opcode argument must be quoted

See test_SubsMat.py and this thread on the mailing list for background:
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011274.html
Tweak doctest for int vs long issue on 64 bit Windows

Rather than (7, 52), Manlio Calvi reports getting (7L, 52L)
with 64 bit Python 2.7 under Windows 7, see mailing list:
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011276.html
Specify encoding for test to pass on Windows

Also minor style changes (PEP8 white spaces).
Update SearchIO blast XML warning test for py3.4 compatibility
Update error message in SearchIO blast-xml warning test
Fix typo in Python 2 vs 3 comment about pickle
Suppress open mode U in as_handle function under Python 3

See strange interaction with warnings in test_SearchIO_blast_xml.py
Don't use mode U under Python 3 now
For Python 3 use raw handles and bytes internally for Bio.trie

This should fix issue #305, test_trie.py was failing on Python 3.4
(although it had worked on Python 3.3).
PEP8 cleanup before real changes
Genepop execution in an isolated, temporary directory (to allow parallel execution)
PEP8 cleanup