[Biopython-dev] Obsolete code

[Michiel de Hoon]

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 Still, it might be good to add a DeprecationWarning there to make people aware that this property is obsolete.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?

--Michiel.

Bio.CelFile.CelParser
Bio.CelFile.CelScanner
Bio.CelFile.CelConsumer
Bio.CelFile.CelRecord

Bio.Align.MultipleSeqAlignment.get_column
Bio.Align.Generic.Alignment
Bio.Align.Generic.Alignment.get_seq_by_num

Bio.AlignAce.Parser

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
(Bio.Blast.NCBIStandalone has been declared obsolete, but I guess some people may still be using the Blast plain-text output parser.)

Bio.Clustalw

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

Bio.Emboss.Applications.EProtDistCommandline
Bio.Emboss.Applications.ENeighborCommandline
Bio.Emboss.Applications.EProtParsCommandline
Bio.Emboss.Applications.EConsenseCommandline
Bio.Emboss.Applications.ESeqBootCommandline

Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.xcentre
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer._set_xcentre
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer.ycentre
Bio.Graphics.GenomeDiagram._AbstractDrawer.AbstractDrawer._set_ycentre
Bio.Graphics.GenomeDiagram._Graph.centre
Bio.Graphics.GenomeDiagram._Graph._set_centre

Bio.Motif.Parsers.AlignAce.AlignAceConsumer
Bio.Motif.Parsers.AlignAce.AlignAceParser
Bio.Motif.Parsers.AlignAce.AlignAceScanner
Bio.Motif.Parsers.AlignAce.CompareAceScanner
Bio.Motif.Parsers.AlignAce.CompareAceConsumer

Bio.Motif.Parsers.MEME.MEMEParser
Bio.Motif.Parsers.MEME._MEMEScanner
Bio.Motif.Parsers.MEME._MEMEConsumer
Bio.Motif.Parsers.MEME._MASTConsumer
Bio.Motif.Parsers.MEME.MASTParser
Bio.Motif.Parsers.MEME._MASTScanner
Bio.Motif.Parsers.MEME.MASTRecord

Bio.PopGen.FDist.RecordParser
Bio.PopGen.FDist._Scanner
Bio.PopGen.FDist._RecordConsumer

Bio.Seq.Seq.data

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