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

[Peter]

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