Separating the old and new Motif code, and adding automatic pwm, pssm calculation to the new Motif class
There shouldn't be any UserWarning from test_SeqIO.py
Speed up PHYLIP output a bit
Disable this bit of testing due to cross platform warning issues.
Refactor common index file opening with BGZF into (private) shared function
GenBank.Scanner: Raise ValueErrors instead of AssertionErrors when parsing fails

Other parts of the parser code all raise ValueError()s when they
encounter unexpected input, just the checks for record.id, record.name
and record.description raise AssertionErrors. Fix this and provide more
meaningful error messages.

For record.name, this code path can be triggered by a GenBank file with
the locus line of "LOCUS        \n".

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Use background as an argument to mean, std, distribution
Adding a test for the TRANSFAC parser
test the degenerate consensus sequence also
Updating the manual
More BGZF testing in SearchIO
Doctest tweak for Python 2,5 on Windows
Updating motif export
Updating the manual for Bio.Motif
Allow parsing of old TRANSFAC files
Fix a typo (use/us) and add links to example script

Documentation change only, no need for TravisCI tests [ci skip]
Clarify tutorial regarding missing GenomeDiagram.GDUtilities

Also added a TODO comment.

Documentation change only, [ci skip] for TravisCI
Exclude some Windows specific problem doctests
Use urlretrieve to smartly download PDB archives

Reading the entire contents into memory with urlopen is a bad idea. With
large crystal structures, it can result in saving an incomplete .gz
archive (raising an Exception on retrieve_pdb_file). Let urllib handle
downloading the file instead.
Use 'with' statement for safer file I/O

Many of the modified functions may be obsolete at this point, but
they're converted to use the more compact, safe 'with' statement. In
Python 2, urllib2.urlopen doesn't implement the 'with' statement, so we
temporarily use contextlib to force this until transition to Python 3.