[Biopython-dev] Deprecations for Biopython 1.61 release; Was: Bio.Motif update

[Peter Cock]

On Mon, Feb 4, 2013 at 12:01 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Fri, Feb 1, 2013 at 3:39 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> --- 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
>
> Bio/SeqIO/SffIO.py function _sff_read_roche_index_xml done:
> https://github.com/biopython/biopython/commit/567464d9a5f8b87ec48e95bae127b86463bd4da1
>
> Bio/File.py and Bio/ParserSupport.py bits done:
> https://github.com/biopython/biopython/commit/63997ea0afa5f7f6cac5c1b036d56416b04edb2a
>
> GenomeDiagram centre setters done:
> https://github.com/biopython/biopython/commit/2424c5ca36cdf4348b54bafdae444a91a6457288

Michiel already did most of the others,
https://github.com/biopython/biopython/commit/1b2025bee868b0282b913690a999833d13598ea4

I've just removed the Seq object's deprecated data property:
https://github.com/biopython/biopython/commit/e3cf12a1bf28c1cd52e4b5492fb1cd76731b486b

For the Seq object's tostring() method, let's review Bow's pull request
after this release? https://github.com/biopython/biopython/pull/137

Regards,

Peter