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

[Michiel de Hoon]

> Would you be thinking of having Bio.Blast.read() and
> parse() only supporting NCBI BLAST+ XML files, or take
> a format argument like we do for sequences and alignments?

I would support BLAST+ XML files only at first, and add parser capability for other formats later if needed. If so, I would use a format argument, same as how Bio.SeqIO works.

> The name of  Bio.Blast.NCBIStandalone is a historical
> relic, and I agree should be retired. Can we label the
> whole of this module as obsolete?

This module also contains the parser for Blast text output, so I think we cannot declare it obsolete just yet. However, if the XML output of BLAST+ is complete, I don't see the need for such a plain-text Blast parser any more.

--Michiel.