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

[Bartek Wilczynski]

Hi,

I'll do the necessary changes in Bio.Motif by the end of the week.

best
Bartek

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.
>



-- 
Bartek Wilczynski
==================
Institute of Informatics
University of Warsaw
http://www.mimuw.edu.pl/~bartek