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

[Tanya Golubchik]

Hello all,

I'm finding that I still use the legacy blastall quite a bit -- I'd be 
very unhappy if it disappeared any time soon. Also, I attempted to use 
the new blast+ but could not immediately make it work. I didn't have 
time to figure out what was going on, but it seemed like it might have 
been to do with my installation of Biopython. At any rate, it would be 
good if these legacy commands could be left alone for the next couple of 
releases at least.

Cheers,
Tanya



Peter wrote:
> Hello all,
> 
> With the release of the new NCBI Blast+ command line tools, the
> existing "legacy" NCBI Blast command line tools are effectively
> being phased out (but will probably still be widely used for some
> time to come).
> 
> Biopython 1.53 included support for the new NCBI Blast+ command
> line tools as wrapper classes in Bio.Blast.Applications for use with
> the Python subprocess module.
> 
> Although labelled as obsolete, Biopython 1.53 also has wrappers
> in Bio.Blast.Applications for the "legacy" Blast tools, and three
> inflexible helper functions in Bio.Blast.NCBIStandalone (blastall,
> blastpgp and rpsblast). Are people still using these? My guess
> is yes, since there were covered in the Biopython tutorial for
> many releases in recent years.
> 
> I recognise this may be premature, but I am suggesting for
> Biopython 1.54 we deprecate the three functions blastall,
> blastpgp and rpsblast in Bio.Blast.NCBIStandalone (and
> encourage people to switch to Blast+ with the wrappers
> in Bio.Blast.Applications instead).
> 
> What do those of you still using Biopython with the "legacy"
> standalone BLAST think? Perhaps we should leave things
> as they are for Biopython 1.54.
> 
> Thanks,
> 
> Peter
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