[BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW

Peter biopython at maubp.freeserve.co.uk
Tue Jul 22 15:38:36 UTC 2008


For any Biopython and Blast users,

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 - even if it doesn't support the current BLAST output
100%. 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) BLAST parser.

Is anyone still using Biopython to parse the HTML output from BLAST?
If so, please speak up.

Peter



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