[Biopython-dev] Obsolete code

[Peter]

On Wed, Aug 25, 2010 at 2:11 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> 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.

No -  bug fixes, documentation are fine.

>> 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 aware that Seq.data is obsolete.

I guess we have to do it at some point, so OK.

>> > 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.

As you pointed out on the other thread, Bio.Fasta has
already been declared deprecated.

Peter