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

[Michiel de Hoon]

Another issue is how the new blast+ affects the Blast parsers. 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.

--Michiel.

--- On Tue, 2/23/10, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] Deprecating Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast functions?
> To: "Biopython Mailing List" <biopython at lists.open-bio.org>
> Date: Tuesday, February 23, 2010, 4:57 AM
> On Mon, Feb 22, 2010 at 5:22 PM,
> Peter <biopython at maubp.freeserve.co.uk>
> wrote:
> >
> > Hi Tanya,
> >
> > Thanks for the feedback - we can postpone the
> deprecation
> > of the Bio.Blast.NCBIStandalone.blastall, blastpgp
> and
> > rpsblast functions for one more release.
> >
> > Deprecation doesn't mean the functionality goes away,
> just
> > you get a warning message that it will in a future
> release
> > go away ;)
> >
> > Regards,
> >
> > Peter
> 
> Hi all,
> 
> I had another couple of replies off list (perhaps
> accidentally),
> one saying they have been slowly moving over to BLAST+
> anyway a deprecation warning from Biopython would
> encourage them, and the second saying delaying the
> deprecation warning would be appreciated.
> 
> So the tentative plan is to add deprecation warnings to
> the Bio.Blast.NCBIStandalone.blastall, blastpgp and
> rpsblast functions in Biopython 1.55 rather then in our
> next release (which will be Biopython 1.54).
> 
> Thanks all,
> 
> Peter
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