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

[Peter]

On Sat, Jan 2, 2010 at 10:44 AM, Kevin Lam <aboulia at gmail.com> wrote:
> Hi all
> finally found
> biopython Wrappers for the new NCBI BLAST+ tools in Applications.py
>
> the question is do I still use NCBIstandalone to use with BLAST+ ?
>

No, use Bio.Blast.Applications with the subprocess module.

>
> is there a new tutorial for this?
>

Did you check the current Tutorial (as shipped with Biopython 1.53)?
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

There are wrappers for the new NCBI BLAST+ tools in the
Bio.Blast.Applications module (recommended for future use).

There are wrappers for the "legacy" NCBI BLAST tools in the
Bio.Blast.Applications module (along with the new BLAST+
wrappers), and the old rather inflexible "helper functions" in
Bio.Blast.NCBIStandalone. These are all effectively obsolete
(since the NCBI is phasing out the "legacy" BLAST tools),
and will be deprecated in a future release of Biopython.
This is in the DEPRECATED file, and the module docstrings.

Obviously the documentation wasn't as clear as it could have
been (and the bit in the tutorial is a little short). Where did you
look and can you make any suggestions for clarification or
improvement?

Thanks,

Peter