[Biopython] Deprecating Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast functions?

[Michiel de Hoon]

> Sounds sensible. Would you be using the existing Record
> classes to hold the output?

Probably not; I don't like the design of the existing Record classes much (in particular, with the Record classes inheriting from Header, DatabaseReport, and Parameters). This is also a good opportunity to remove inconsistencies between attribute names between the different parsers. The DTD of the blast XML output can help us to decide on appropriate attribute names.
That said, I expect that from a user perspective there will be little difference between an old-blast Record and a blast+ Record. For the development, I was thinking of setting up the parser step by step, and to discuss on the mailing list if any potential differences arise with the existing parsers.

> We've been referring to the plain text BLAST parser as
> obsolete or deprecated in the documentation for some
> time now (although there isn't yet an actual deprecation
> warning issues). So I don't see a problem with calling
> the whole of Bio.Blast.NCBIStandalone obsolete.

I don't have any strong objections here, so as far as I am concerned feel free to declare Bio.Blast.NCBIStandalone obsolete.

--Michiel