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.
Phylo.draw_ascii: use floor division (Py3 compatibility)

See Bug #3435
Using // for explicit integer division, don't need import
SeqIO: Better cope with wrong LOCUS line spacing in GenBank

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>
Fix minor typo in exception
Thank Kai for GenBank parsing work
For Python 3, recommend Python 3.3.2 or later
Run part of test_Phylo_depend.py if NetworkX missing
Merge remote-tracking branch 'upstream/master' into samtools_wrapper