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.
Skip tests for 'bwa aln' when 'aln' is unrecognized

'bwa aln' is failing for bwa[0.7.6a-r433], see:
http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011342.html