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

[Kevin Lam]

On Tue, Jan 12, 2010 at 1:08 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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.
>

Yes I was thinking of this when i meant porting/integrate. to integrate the
legacy blast perl script into  Bio.Blast.NCBIStandalone

I didn't realise that Bio.Blast.Applications existed

> 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
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc80
was exactly what I was looking for! Maybe i was looking at the wrong page
Thanks for pointing it out!



> Thanks,
>
> Peter
>

Cheers
Kevin