[Biopython-dev] Where to put command line wrappers

[Peter]

>  I see introducing Bio.Align.Applications as chance to get a more
>  consistent approach to Biopython's command line wrappers established
>  (replacing Bio.Clustalw).  And as I wrote last month, I think we
>  should focus on the Bio.Application command line wrapper object.  For
>  reasons explained in the linked email, I would want to rewrite
>  Bio.Blast.NCBIStandalone in the same way (probably putting the command
>  line wrapper classes in Bio.Blast.Applications, and if there is
>  interesting, include other variants like WUBlast).  Are there any
>  other wrappers not using Bio.Application which I have forgotten about?

Funnily enough, there already is a Bio.Blast.Applications module
containing a wrapper for NCBI Fasta and NCBI blastall (a little out of
data, also nothing for rpsblast or blastpgpg).  The older
Bio.Blast.NCBIStandalone was never updated to use this internally.
Here's a nice little job for after Biopython 1.50 is out...

Peter