Patch blast 2.2.27+ wrapper

[bow]

Per http://lists.open-bio.org/pipermail/biopython-dev/2013-February/010306.html

[peterjc]

I've applied 3 of the 4 commits, tested with BLAST 2.2.26+ which meant a little modification to test_NCBI_BLAST_tools.py as done previously - the primary goal of the CheckCompleteArgList class is really just to alert us to when the wrapper needs updating.

I'm not sure we should just remove the -frame_shift_penalty option as it still exists on the older versions of BLAST+, probably just adding a comment about this to the docstring would suffice (and ignore this in test_NCBI_BLAST_tools.py)?

[bow]

To maintain compatibility with older BLAST+ versions, yes, I agree we should keep the obsolete command line args.

I was probably taking the warnings too seriously and removed these extra arguments. And yes, a note in the docstring should suffice.

[peterjc]

Done: 63997ea

Thanks

[bow]

Great :), thanks Peter.