[Biopython-dev] Bio.Motif update

[Michiel de Hoon]

--- On Fri, 2/1/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> I went over the list in the DEPRECATED file last month, but
> a second check would be a good idea.

The following were declared obsolete in Biopython 1.60, and can in principle be declared deprecated in Biopython 1.61:

----------
Bio/Blast/Applications.py:
BlastallCommandline
BlastpgpCommandline
RpsBlastCommandline

Bio/Blast/NCBIStandalone.py overall, and specifically:
blastall
blastpgp
rpsblast

Bio/ParserSupport.py overall

Bio/PDB/AbstractPropertyMap.py:
The has_key function in class AbstractPropertyMap

Bio/PDB/FragmentMapper.py:
The has_key function in class FragmentMapper

Bio/UniGene/UniGene.py overall

In BioSQL/BioSeqDatabase.py:
  class DBServer:
     remove_database
  class BioSeqDatabase:
     get_all_primary_ids
     get_Seq_by_primary_id

-----------

These functions were deprecated in Biopython 1.59 or earlier, and could be removed for Biopython 1.61:

Bio/Align/__init__.py:
  class MultipleSeqAlignment:
     get_column
     add_sequence

Bio/Align/Generic.py:
  class Alignment overall
    get_all_seqs
    get_seq_by_num

Bio/File.py:
  class StringHandle

Bio/Graphics/GenomeDiagram/_AbstractDrawer.py:
  class AbstractDrawer:
    _set_xcentre, _set_ycentre

Bio/Graphics/GenomeDiagram/_Graph.py:
  class GraphData:
    _set_centre

Bio/ParserSupport.py:
  SGMLStrippingConsumer

Bio/Seq.py:
  class Seq:
     .data property

Bio/SeqIO/SffIO.py:
  _sff_read_roche_index_xml
 
--------------------

The tostring() method of the class Seq in Bio/Seq.py:
Can we declare this obsolete?

-Michiel