[Biojava-l] status? Blast parser?

Jeffrey Chang jchang@SMI.Stanford.EDU
Wed, 16 Feb 2000 12:39:09 -0800 (PST)

On Wed, 16 Feb 2000, Simon Brocklehurst wrote:

> I'm open to suggestion here - if people want to use biopython conventions for
> metadata, that's what we'll do.  What about the bioxml proposal on BLAST XML
> element naming from the guys at SB? Is this similar to the biopython stuff?

The bioxml BLAST XML DTD proposal is a way to mark up information found
within a blast document, while the biopython stuff, oriented toward
line-oriented parsers, is a way to mark up lines inside a blast document.
The semantics are subtly different.  For example, the blast xml has
separate entities that describe the blast program name and version.
However, since those (currently) appear on the same line in the output,
biopython has only 1 event associated with it:
version        : BLASTP 2.0.10 [Aug-26-1999]

Thus, the XML DTD is for a later stage in processing than the biopython
consumer events.  Which one is appropriate depends on how the parser is