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

[Peter Cock]

On Apr 29, Peter wrote:
> On Apr 29, 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.  ...
>
> If you where asking about the actual code for how to build the command
> line object, well I have some thoughts on making the current
> Bio.Application base class easier to use (properties and keyword
> arguments at init) which I have started to discuss on the dev list.

See this dev list thread:
http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005916.html

And Bug 2822 (with examples):
http://bugzilla.open-bio.org/show_bug.cgi?id=2822

Peter