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

[Peter]

On Mon, Mar 1, 2010 at 9:40 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> --- 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.

That is a very practical solution to the problem. Chuckle.

>> 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.

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.e.
What about other formats like the old NCBI XML (if it has
changed), the assorted tabular BLAST outputs, non-NCBI
BLAST, and finally the still sometimes useful plain text
output (e.g. for use with third party tools like BLAT).

> 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).

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? As discussed earlier on this thread people are
still using it for calling BLAST so we won't deprecate it in the
next release (but likely the one after that).

Peter