[Biopython-dev] Bio.Motif update

[Peter Cock]

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

My impression is there is still a sizeable group of people still using
blastall and the rest of legacy BLAST as it is mature reliable code,
while BLAST+ still has some rough edges. But as the NCBI themselves
have now stopped updating legacy BLAST, perhaps the time has come.

So if you want, deprecating the legacy BLAST wrappers seems OK.

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

Given the SearchIO use of the plain text BLAST parser, I think we
agreed to leave that as is in the short term.

The command line calling functions blastall, blastpgp & rpsblast
the same applies as for BlastallCommandline, BlastpgpCommandline
and RpsBlastCommandline (above).

> Bio/ParserSupport.py overall

Given the SearchIO use of the plain text BLAST parser which uses
this, I think we agreed to leave that as is in the short term.

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

The Python dict lost the has_key function in Python 3, so it does
make sense to proceed with those deprecations.

> Bio/UniGene/UniGene.py overall
>

Yes, ready to deprecate.

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

Yes, ready to deprecate.

Thanks,

Peter