[Biopython-dev] Deprecating the HTML parser in Bio.Blast.NCBIWWW

[Peter]

For some time now we've been discouraging the use of the HTML and
plain text Blast parsers in favour of the XML format.

I think it would be a good idea to now officially deprecate the HTML
parser in Bio.Blast.NCBIWWW with warning messages when it is used.  I
don't even know if it still works with the recent big revision to the
BLAST webpages, but I suspect not.

However, the plain text parser in Bio.Blast.NCBIStandalone still has
its uses.  In particular, right now the PSI-BLAST output in XML format
lacks some of the information found in the plain text output (new vs
reused entries) so it would be premature to deprecate our plain text
PSI parser.  See Bug 2502 for details:
http://bugzilla.open-bio.org/show_bug.cgi?id=2502#c18

Peter