[Biopython-dev] Pending deprecations

[Michiel de Hoon]

Hi everybody,

The following bits of code have a PendingDeprecationWarning in release 1.56. Any objections to upgrading those to BiopythonDeprecationWarnings for the next release? That would mean that users see a deprecation warning by default when using those pieces of code.

Bio.Align.MultipleSeqAlignment.get_column
Bio.Align.MultipleSeqAlignment.add_sequence
Bio.Align.Generic.Alignment.__init__
Bio.Align.Generic.Alignment.get_seq_by_num
Bio.Blast.Applications.BlastallCommandline
Bio.Blast.Applications.BlastpgpCommandline
Bio.Blast.Applications.RpsBlastCommandline
Bio.Blast.NCBIStandalone
Bio.Blast.NCBIStandalone.blastall
Bio.Blast.NCBIStandalone.blastpgp
Bio.Blast.NCBIStandalone.rpsblast
Bio.Clustalw.parse_file
Bio.Clustalw.do_alignment
Bio.ClustalW.ClustalAlignment
Bio.ClustalW.MultipleAlignCL
Bio.File.SGMLStripper
Bio.Nexus.Nexus._kill_comments_and_break_lines
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper.FragmentMapper.has_key
BioSQL.BioSeqDatabase.DBServer.remove_database
BioSQL.BioSeqDatabase.BioSeqDatabase.get_all_primary_ids
BioSQL.BioSeqDatabase.BioSeqDatabase.get_Seq_by_primary_id

We were also planning to add a PendingDeprecationWarning to
Bio.Seq.Seq.tostring, but this will require to replace all calls to my_seq.tostring() in Biopython by str(my_seq). It would be good to start doing this in your favorite Biopython module.

Best,
--Michiel.