[Biopython-dev] Obsolete code

[Bartek Wilczynski]

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 aware that this property is obsolete.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
>
>
>
>
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>
>


-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433