[Biopython-dev] Deprecated code

[Michiel de Hoon]

I finished adding the deprecation warnings and removing deprecated code as discussed, except for these three:

Bio.Transcribe
Bio.Translate
BioSQL.BioSeqDatabase.open_database: driver="psycopg" option

For last one, I wasn't sure how to appropriately remove this option from the code. Maybe somebody more familiar with BioSQL can take care of this?

For Bio.Transcribe and Bio.Translate, it turned out that Bio/Encodings/IUPACEncoding.py still use these modules. I don't know if Bio.Encodings.IUPACEncoding is still being used. It's only imported from Bio.Alphabet.IUPAC, but it doesn't seem to be actually used there. Bio.Encodings itself is not being imported anywhere in Biopython.

Can we declare Bio.Encodings obsolete? Or can we just remove this module together with Bio.Transcribe, Bio.Translate?

--Michiel.

--- On Sat, 8/21/10, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> From: Michiel de Hoon <mjldehoon at yahoo.com>
> Subject: [Biopython-dev] Deprecated code
> To: biopython-dev at biopython.org
> Date: Saturday, August 21, 2010, 2:56 AM
> Dear all,
> 
> Below are the modules and functions that were deprecated
> (with a DeprecationWarning) in Biopython 1.51 or earlier,
> which was released on August 17, 2009. Since that is more
> than one year (and more than two releases) ago, we can
> remove these from Biopython. Any objections? If not, I'll
> send this list also to the user mailing list before removing
> them.
> 
> --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
> 
> 
> 
>       
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