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

[Michiel de Hoon]

--- On Sat, 2/27/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
> I hadn't realised the NCBI had changed the XML. I
> wonder if multiple query PSI-BLAST output works
> nicely now?

The psiblast program as part of blast+ doesn't allow multiple queries, so in that sense the problem was disappeared.

> If the existing NCBI XML parser can cover both variants,
> then it makes more sense to me to continue to use the
> existing read & parse functions under
> Bio.Blast.NCBIXML.

Well I was thinking that this is a good time to tackle all outstanding Blast parser bugs & issues, which may break consistency with the existing parsers. So I would prefer to copy the code in Bio.Blast.NCBIXML, modify it as needed for blast+, and in some future Biopython release (not anytime soon) to deprecated NCBIStandalone and NCBIXML. In any case, I think it is nicer to have a read() function directly under Bio.Blast, so I don't have to remember and type in the names of the submodules NCBIXML and NCBIStandalone (the name of the latter doesn't make much sense anyway).

--Michiel.