[Bioperl-l] DEPRECATED list

[Chris Fields]

One last day to respond; I'll start removing the modules scheduled  
below tomorrow (already have removed their dependencies from Build.PL).

chris

On Dec 8, 2008, at 11:00 PM, Chris Fields wrote:

> The following modules are slated to be removed for the 1.6 release:
>
>                          Version    Version
> Deprecated Modules       Deprecated  Removed Comment
> --------------------------------------------------------------------------------
> Bio::Tools::RestrictionEnzyme 1.5      1.6    use Bio::Restriction
> Bio::Tools::BPlite            1.5      1.6    use Bio::SearchIO
> Bio::Tools::BPpsilite         1.5      1.6    use Bio::SearchIO
> Bio::Tools::BPbl2seq          1.5      1.6    use Bio::SearchIO
> Bio::Ontology::SimpleGOEngine 1.5.1    1.6    use  
> Bio::Ontology::OBOEngine
> Bio::Factory::ResultFactoryI  1.5.2    1.6    Superseded by  
> Bio::Factory::ObjectFactory
> Bio::Factory::HitFactoryI     1.5.2    1.6    Superseded by  
> Bio::Factory::ObjectFactory
> Bio::Graph                    1.5.2    1.6    Superseded by bioperl- 
> network
> Bio::Tools::WebBlat           1.5.2    1.6    Requested that this  
> not be maintained
> Bio::DB::XEMBL                1.5.2    1.6    Service no longer  
> available; use DBFetch
> Bio::DB::XEMBLService         1.5.2    1.6    Service no longer  
> available; use DBFetch
>
> The following are to be added to the deprecation list:
>
> Bio::Tools::RNAMotif          1.5.2    1.7    Superseded by  
> Bio::SearchIO::rnamotif
> Bio::Tools::Infernal          1.5.2    1.7    Superseded by  
> Bio::SearchIO::infernal
> Bio::Tools::ERPIN             1.5.2    1.7    Superseded by  
> Bio::SearchIO::erpin
>
> Were there any others we should recommend?  I noticed Bio::Species  
> isn't on the list for 1.7.  I also suggest Bio::Search::BlastUtils  
> (it is the same as Bio::Search::SearchUtils, but older).
>
> chris
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