[Biopython] Deprecated code to be removed from Biopython

[Michiel de Hoon]

Dear all,

Below are the bits of code in Biopython that are currently deprecated (with a DeprecationWarning). These have been deprecated since Biopython 1.51, and we are considering to remove them completely for the final release of Biopython 1.55. Any objections? Is anybody still using any of this code?

Thanks,
--Michiel.

Bio.Align.FormatConvert
Bio.Emboss.Applications.PrimerSearchCommandline.set_parameter
Bio.Entrez.efetch: rettype="genbank" option
Bio.Fasta
Bio.SCOP.Dom.Parser
Bio.SwissProt.SProt
Bio.Transcribe
Bio.Translate
BioSQL.BioSeqDatabase.open_database: driver="psycopg" option