Avoid the sub_features deprecation warning in these methods.

This was being triggered in for example SeqRecord addition of
GenBank records.
Update MANIFEST to include Doc/examples/my_blast.xml

This was missing in Biopython 1.61, reported on the mailing list
http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010599.html
by Lin (林行众).
Update MANIFEST to include Doc/examples/my_blat.psi

Identified by Lin (林行众) on the mailing list - thanks!
http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010601.html
Fix testing with clustalw 1.83

Old test worked with clustalw 2.1 but the behaviour of 1.83 was
slightly different leading to the unit test wrongly failing:
http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010599.html
Skip test_bgzf.py if Python's gzip is broken
Skip Bio.bgzf doctest if gzip broken http://bugs.python.org/issue17666
Can't import anything from Bio in run_tests.py
Revert moving import (must be after edit PYTHONPATH)
Stupid typo, broken under Python 3
Skip BGZF tests in test_SeqIO_index.py if issue 17666
Updated FastaWriter documentation to reflect reality

Someone must have edited the code and didn't update the documentation for FastaWriter.
Added color_scheme keyword to weblogo to allow users to set their own colors (suggested by Anthony Mathelier of UBC)
added a gc_content method method to the GenericPositionMatrix in Bio.motifs (contributed by Anthony Mathelier of UBC)
removed some whitespace
Avoid NaN results if p is zero
Two blank lines between classes (PEP8)
Fix lots of overly long lines, try to follow PEP8 for property docstrings
Omit argument with default value
Adding static argument to Bio.Application, use for BWA
Fix for missing isnan on Python 2.5