[Bioperl-l] 0.7 release: Blast

Ian Korf ikorf@sapiens.wustl.edu
Tue, 14 Nov 2000 15:29:47 -0600 (CST)

On Tue, 14 Nov 2000, Paul Gordon wrote:

> > 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.
> Yes, it will take a while for that to stabalize.  There are still quite a
> few issues with the lossiness of the XML from Blast that I've been meaning
> to send them...
> Anyway, although that would certainly be a nice way to do it (XML queries
> on the document for each method instead of parsers), I don't think that
> such a module would replace the current one because there are lots of
> people who won't want to produce XML reports for one reason or another,
> especially people using command line Blast and looking at the text
> reports.

I agree. I think you could draw an analogy between BLAST reports/BLAST XML
DTDs and GenBank flat file/GenBank ASN.1. I'm sure that ASN.1 is superior
to the flat file, and I'm sure that XML will be superior to the BLAST
report, but I have to admit that I use the flat files more often than the