Test command line wrapper handling of stdout/stderr
Must open /dev/null for writing.

Very curious that this didn't cause a problem with stdout,
just stderr. Thank you to Lenna and Saket for spotting this
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010488.html

Finding and fixing this unreported bug was a nice bonus from
writing test_Application.py :)
Allow command line wrappers to send stdout/stderr to files

See mailing list discussion (useful for bwa etc)
http://lists.open-bio.org/pipermail/biopython-dev/2013-February/010399.html
Python 2.5 with statement support
Prank: PEP8 whitespace cleanup.
Move a docstring to the right place.
Remove superfluous commas.
Use SeqUtils.seq1() instead of SCOP.to_one_letter_code().
Some grammar improvements.

Peter: Resolved conflicts during merge
Wrap some long lines in the Tutorial source
Thank Christian Brueffer for misc fixes
Revert "Use SeqUtils.seq1() instead of SCOP.to_one_letter_code()."

This reverts commit ca7762e8247dbcd6b3cbc6d0a7082eaf36dceb46.

It was causing test failure in some of the PDB code due to not
handling all the 'odd' three letter codes for modified amino
acids. I was too hasty in checking this in... opps.