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

[Peter]

On Sat, Feb 27, 2010 at 5:52 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Another issue is how the new blast+ affects the Blast parsers.

I made some updates to the plain text parser, enough to
work on the simple examples I tried. We and the NCBI
still recommend people to use the XML output.

> I've looked at the XML output and it looks cleaner than the
> XML output of the older blast. At least, it tells us if blast or
> psiblast was used, which allows us to figure out how the file
> should be parsed. I suggest we create a read() and parse()
> function under Bio.Blast to parse the output of blast+, and
> leaving the existing parsers untouched. If this looks like a
> good idea, I can get started and set up a skeleton read(),parse()
>  function for now.

I hadn't realised the NCBI had changed the XML. I
wonder if multiple query PSI-BLAST output works
nicely now?

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.

Peter