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
Switch import testing order for Bio.Cluster test
Clean up test files after running BWA & samtools tests
Put return code at start of Bio.Application error message.

This is in case the ApplicationError exception message
gets truncated and this information is lost (e.g. due to
a very long command line from several long file names).
Just use relative paths in this test
Update due to changed Bio.Application error message
Match case; I should install this dependency locally...
More side effects from changing exception...

Also show actual error if assert fails.
TravisCI now supports Python 3.4
Close these handles
Comment regarding rU mode and Python 3
Avoid open(filename, 'rU') on Python 3

Perhaps some of these examples can be just mode 'r' on Python 2?
We would need more testing under Windows to be sure through...
newline characters are a pain.