[Biopython-dev] Obsolete code

[Michiel de Hoon]

I applied your patch to Bio.Motif, and added DeprecationWarnings to each of the submodules of Bio.AlignAce (without them, importing one of the submodules directly did not issue the DeprecationWarning in Bio.AlignAce.__init__).

Thanks,
--Michiel.

--- On Sat, 8/21/10, Bartek Wilczynski <bartek at rezolwenta.eu.org> wrote:

From: Bartek Wilczynski <bartek at rezolwenta.eu.org>
Subject: Re: [Biopython-dev] Obsolete code
To: "Michiel de Hoon" <mjldehoon at yahoo.com>
Cc: biopython-dev at biopython.org
Date: Saturday, August 21, 2010, 4:56 AM

Hi, 

Great job. 

I just have a small comment on the Bio.AlignAce.Parser module. It is a part of the Bio.AlignAce "package" which was  already deprecated  (see Bio.AlignAce.__init__.py). I think either there is no need to put an extra deprecation warning in Bio.AlignAce.Parser, or we should put it in all submodules of Bio.AlignAce (like Bio.AlignaAce.Motif, etc.).


As for deprecating the old parsers in Bio Motif, I've just looked through the code in Motif.__init__.py and realized that it was still using the old implemmentations...

This small patch below should fix it (I don't want to push onto the main branch now, as it's frozen). 


Cheers
Bartek

diff --git a/Bio/Motif/__init__.py b/Bio/Motif/__init__.py
index 4c7c19a..9ca0200 100644
--- a/Bio/Motif/__init__.py
+++ b/Bio/Motif/__init__.py
@@ -10,12 +10,12 @@ as well as methods for motif comparisons and motif searching in sequences.

 It also inlcudes functionality for parsing AlignACE and MEME programs
 """
 from _Motif import Motif
-from Parsers.AlignAce import AlignAceParser, CompareAceParser
-from Parsers.MEME import MEMEParser,MASTParser

+import Parsers.AlignAce 
+import Parsers.MEME 
 from Thresholds import ScoreDistribution
 
-_parsers={"AlignAce":AlignAceParser,
-          "MEME":MEMEParser
+_parsers={"AlignAce":Parsers.AlignAce.read,

+          "MEME":Parsers.MEME.read
           }
 
 def _from_pfm(handle):
@@ -75,7 +75,7 @@ def parse(handle,format):
         else: #we have a proper reader 
             yield reader(handle)

     else: # we have a proper reader
-        for m in parser().parse(handle).motifs:
+        for m in parser(handle).motifs:
             yield m
 
 def read(handle,format):



On Sat, Aug 21, 2010 at 8:30 AM, 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?



--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











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-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
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