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.
Can't use context manager with gzip.open until Python 2.7 (reported by Bryan Lunt)
Skip test failing due to http://bugs.python.org/issue16903

Rather than adding a workaround to the code, we'll probably
just set a minimum verion of Python 3 instead.
Added the capability to set the number of pseudocounts equal to the square root of the number of instances
Also skip test_PopGen_DFDist.py if on old Python 3

See earlier commit 9c16c09806ca4af84f714662e54c9bd3057b0a52 for
test_PopGen_FDist.py to skip the test if on an older Python 3
with http://bugs.python.org/issue16903
Fix Bio.ExPASy.ScanProsite.read in Python 3.

ScanProsite.read fails on Python 3, this fix is backwards compatible
with Python 2.
Merge pull request #184 from luizirber/master

Fix for ScanProsite.read, works with Python 2 and 3
code for dealign with assorted UniProt file formats; contributed by Iddo Friedberg.
New module Bio.UniProt in NEWS file
Must install the new Bio.UniProt module
Expanded jaspar module contributed by Anthony Mathelier and David Arenillas of UBC
fixed a few typos
Add the new Bio.motifs.jaspar package to the list of packages to install
Fix doctest which was blocking 2to3 and preventing installation on Python 3
Assume stranded features for bad LOCUS link GenBank files.

i.e. Default to assuming nucleotides (and so stranded features)
rather then amino acids (where the protein features have no strand)

Based on an issue reported by Kai Blin.

Unit test to follow...
Adding test case from Kai Blin; Fixed some warnings.

This test GenBank file with an invalid LOCUS line lets
us test the strand behaviour fixed in the previous
commit.

Some generic warnings from the GenBank parser should
have been BiopythonParserWarning - and thus silenced
in the unit tests.

Also fixed line lengths for some other GenBank warnings.