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

[Tiago Antão]

I will do it over the weekend for bio.popgen

2011/8/11, Peter Cock <p.j.a.cock at googlemail.com>:
> 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.
>

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