[Biopython] is there an updated tutorial on how to use the Wrappers for the new NCBI BLAST+ tools?

[Peter]

On Mon, Jan 11, 2010 at 4:46 PM, Kevin <aboulia at gmail.com> wrote:
> Hi Peter,
> I was thinking of porting the legacy blast script to python as u r right
> about the helper script being inflexible.

A python version of legacy_blast.pl isn't any more useful than the
Perl version is it? Maybe I have misunderstood you.

What would be nice is a way to help people update their old
Biopython scripts which called legacy BLAST, so that they can
be used on BLAST+ instead. I would expect in most cases this
means scripts using the legacy BLAST "helper" functions in
Bio.Blast.NCBIStandalone. One way to do this would be to
add new BLAST+ versions of the "helper" functions (taking
the same argument names as before), but that is just a stop
gap (a temporary measure). We really want people using these
old helper functions to switch to using the wrappers in
Bio.Blast.Applications and subprocess instead.

> The documentation bit was actually about my first email about any
> updated doc on how to use blast+ with biopython

I see. What do you think the current (Biopython 1.53) version
of the tutorial needs in the BLAST chapter?

http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

Thanks,

Peter