Patch for Python 3 support with Popen.communicate
committed patch from bug report #3433 by Alexander Campbell. Also removed the requirement for Flex in test_MMCIF.
The MMCIF parser is pure-Python nowadays
Thank Alexander Campbell (report and fix for issue 3443 in MMCIFParser)
Revert "Patch for Python 3 support with Popen.communicate"

This reverts commit 912692ee2b57e8c075ba38bdf814c9dbe4f5cdb9.

Unfortunately while the 'fix' made things work on Python 3.1
and old versions of Python 3.2, it breaks on Python 3.2.4
onwards and Python 3.3 and Windows. We should be using (unicode)
strings if calling subprocess with universal_newlines=True
but were hitting a Python bug, http://bugs.python.org/issue16903

See mailing list discussion:
http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010626.html

On option is not to support the older broken Python 3 releases.
Another choice is to use universal_newlines=False and handle
the bytes/unicode conversion explicitly for stdin/stdout/stderr.