[Biopython-dev] [Biopython] Parsing large blast files

[Peter]

Last month on this thread we started talking about the BLAST
command line wrappers:
http://lists.open-bio.org/pipermail/biopython/2009-April/005134.html

On Wed, Apr 29, 2009, Peter wrote:
> On Wed, Apr 29, 2009, Michiel de Hoon wrote:
>>
>> How would users typically use Bio.Blast.Applications?
>
> In the next release, I would aim to have Bio.Blast.Applications
> updated to cover blastall (fully), plus blastpgp and rpsblast
> (currently not covered) and for the three helper functions
> Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast to all use
> Bio.Blast.Applications internally.

That should be done now in CVS - it turned out to be a lot more
tedious that I had expected, but I think we are OK.

I would be very grateful to have a couple of people test this out.
At the very least, just update your copy of Biopython and confirm
any existing scripts using the Bio.Blast.NCBIStandalone
blastall, blastpgp or rpsblast functions still work as expected.

Note we still need to agree on the preferred name for each
parameter (i.e. what do we use for the python properties) as
discussed on this thread:
http://lists.open-bio.org/pipermail/biopython-dev/2009-May/005976.html
http://lists.open-bio.org/pipermail/biopython-dev/2009-May/006039.html

Peter