[Biopython] Deprecated code to be removed from Biopython

[Andrew Perry]

On 25 August 2010 23:52, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> 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
>
>
No objections here. I did a quick grep over some of my code from the last
two or three years - while I'm still using things
like Bio.Align.FormatConvert (probably because I was cut and pasting from
even older code), and Bio.SwissProt.SProt in some even older scripts, a
quick look at the API documentation for these deprecated parts provides
clear and simple pointers on how to migrate, so I'm happy.

Good work on the docs in this respect !

Andrew Perry