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

[Peter]

On Tue, Mar 2, 2010 at 10:01 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
>> 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.

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

>> 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.

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 think we can add deprecation warnings to the
plain text parser yet. While the XML format(s) are better
for parsing, there are still corner cases where the plain
text has advantages (file size, BLAST like output from
non-NCBI tools like BLAT, NCBI psi-blast output
although they have apparently improved the XML
here).

We also should worry about non-NCBI BLAST tools
and their output.

Peter