[Biopython-dev] Deprecated code in Bio.PopGen and Bio.Motif ready to go?

[Peter Cock]

Hi Tiago & Bartek,

Looking over the DEPRECATED file, the following are about due for removal
in Bio.PopGen and Bio.Motif - do you guys have time to make these changes
yourselves?

Thanks,

Peter

> Bio.PopGen.FDist
> ================
> The RecordParser, _Scanner, and _RecordConsumer classes were declared obsolete
> in Release 1.54, and deprecated in Release 1.55 final. Their functionality is
> now available through a read() function.

and:

> Bio.Motif
> =========
> ...
> AlignAceConsumer, AlignAceParser, and AlignAceScanner were declared obsolete
> in Release 1.53 and deprecated in Release 1.55 final; their functionality is
> now available through a read() function in Bio.Motif.Parsers.AlignAce.
> MEMEParser, _MEMEScanner, _MEMEConsumer, _MASTConsumer, MASTParser,
> _MASTScanner, and MASTRecord were declared obsolete in Release 1.54 and
> deprecated in Release 1.55 final; their functionality is now available through
> a read() function in Bio.Motif.Parsers.MEME and Bio.Motif.Parsers.MAST,
> respectively.

P.S. We don't usually need to mention private classes like _MEMEScanner in
the DEPRECATE file.