[Bioperl-l] 0.7 release: Blast

Aaron J Mackey ajm6q@virginia.edu
Tue, 14 Nov 2000 14:03:49 -0500 (EST)

On Tue, 14 Nov 2000, Ewan Birney wrote:

> What do we do -
> 	- battle on with blast modules?
> 	- fork bplite?
> 	- rewrite?

My humble suggestion is to wait a little longer until XML output becomes
stable, and then write a new Blast parser which uses the DTD to parse the
file and build the respective necessary data storage object(s).  Then
deprecate the use of the old Blast parsing (I'd guess that those who use
BioPerl for large scale blast parsing would also be able to control their
blast output format option), in favor of XML-parsing.

In short, don't spend time reinventing an ancient wheel - wait a little
longer and invent and invent a more modern (and easier to build) wheel.


P.S. I'll reiterate our desire for someone to present us with a Grand
Unified DTD for sequence comparison/alignment, usable by both Blast and
FASTA and others ... and then tell us how after meeting the spec of the
DTD, we can extend it for our own internal purposes (data types that the
rest of the world probably won't care about and therefore shouldn't be in
the grand unified dtd).