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

[Peter]

On Tue, Mar 2, 2010 at 3:45 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
>> 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).

Yes, that is odd.

> This is also a good opportunity to remove inconsistencie
> between attribute names between the different parsers.
> The DTD of the blast XML output can help us to decide
> on appropriate attribute names.

Again, this is worthwhile (i.e. fix Bug 2176).
http://bugzilla.open-bio.org/show_bug.cgi?id=2176

> 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.

Great :)

>> 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.

Done in the repository.

Peter