[Biopython-dev] Obsolete code

[Peter Cock]

On Saturday, August 21, 2010, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Dear all,
>
> The classes and modules listed below were declared obsolete in Biopython 1.54 or earlier, but do not yet raise a deprecation warning. Most of this functionality moved to a different module or was implemented differently. I suggest we add a DeprecationWarning to each of these before Biopython 1.55 final. The only tricky one is the .data property of Seq classes in Bio.Seq. Still, it might be good to add a DeprecationWarning there to make people aware that this property is obsolete.
>
> Any objections?

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.

>
> --Michiel.
>
> Bio.CelFile.CelParser
> Bio.CelFile.CelScanner
> Bio.CelFile.CelConsumer
> Bio.CelFile.CelRecord
>

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.

> Bio.AlignAce.Parser

Ok

>
> 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.

> (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?

>
> Bio.Clustalw

Ok

>
> Bio.Compass._Scanner
> Bio.Compass._Consumer
> Bio.Compass.RecordParser
> Bio.Compass.Iterator

Ok

> Bio.Emboss.Applications.EProtDistCommandline
> Bio.Emboss.Applications.ENeighborCommandline
> Bio.Emboss.Applications.EProtParsCommandline
> Bio.Emboss.Applications.EConsenseCommandline
> Bio.Emboss.Applications.
> Bio.Align.FormatConvert
> Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter
> Bio.Entrez.efetch: rettype="genbank" option

Should be fine.

> Bio.Fasta

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

> Bio.SCOP.Dom.Parser
> Bio.SwissProt.SProt
> Bio.Transcribe
> Bio.Translate
> BioSQL.BioSeqDatabase.open_database: driver="psycopg" option

Ok

>
> Bio.SeqUtils.GC_Frame
> Bio.SeqUtils.fasta_uniqids
> Bio.SeqUtils.apply_on_multi_fasta
> Bio.SeqUtils.quicker_apply_on_multi_fasta
>
> Bio.UniGene.UnigeneSequenceRecord
> Bio.UniGene.UnigeneProtsimRecord
> Bio.UniGene.UnigeneSTSRecord
> Bio.UniGene.UnigeneRecord
> Bio.UniGene._RecordConsumer
> Bio.UniGene._Scanner
> Bio.UniGene.RecordParser
> Bio.UniGene.Iterator
>

Ok

Apologies for brevity and any typos, this was sent from an iPod.

Peter