Use filenames with SeqIO.read in Tutorial

Documentation change only - Travis [ci skip]
Close handles; More explicit error messages
Forgot the Python 2.5 with_statement import
Refactor test_BWA_tool.py - may fix random buildbot failures.

Method test_aln(...) is now not a test in its own right, but
only called from test_sampe.

Error messages now more verbose to try and explain any further
failures.
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)