[Biopython-dev] Obsolete code

[Michiel de Hoon]

Tiago, Bartek, Peter,

Thanks for your comments.

Peter, is the main branch still frozen? I'd like to make these changes on Saturday Japanese time, so Friday night in Europe/US.

> I'd be cautious about the Seq object given it will be
> particularly widely used. I've commented on a few cases
> below, but in general yes deprecation of things previously
> marked as obsolete is sensible house keeping.

For the Seq object, I think it's good to have a DeprecationWarning to make users aware of the changes. For example, I was not aware that Seq.data is obsolete.

> > Bio.Align.MultipleSeqAlignment.get_column
> > Bio.Align.Generic.Alignment
> > Bio.Align.Generic.Alignment.get_seq_by_num
> 
> I'd like to make the new alignment object a bit more user
> friendly before we deprecate these bits.

OK I won't touch these then.

> > Bio.Blast.Applications.FastacmdCommandline
> > Bio.Blast.Applications.BlastallCommandline
> > Bio.Blast.Applications.BlastpgpCommandline
> > Bio.Blast.Applications.RpsBlastCommandline
> > Bio.Blast.NCBIStandalone.blastall
> > Bio.Blast.NCBIStandalone.blastpgp
> > Bio.Blast.NCBIStandalone.rpsblast
> 
> The NCBI are still supporting "legacy" BLAST so it is
> probably a bit too early to deprecate these wrappers.
> Maybe I'm being cautious but I'd leave this until the
> next release in three months time or so.

OK.
 
> (Bio.Blast.NCBIStandalone has been declared obsolete,
> but I guess some people may still be using the Blast
> plain-text output parser.)
> 
> Deprecation seems premature - the code is still useful and
> probably widely used (I use it myself sometimes). Maybe once your
> new BLAST parsing framework is ready Michiel?

OK.

> > Bio.Fasta
> 
> Here my instinct is to be cautious given Bio.Fasta used to
> be such a widely used module.

Here also I think we should make our users aware of the changes, especially because it used to be widely used.

--Michiel.