[Bioperl-l] DEPRECATED list

[Chris Fields]

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Bio::Factory::ResultFactoryI  1.5.2    1.6    Superseded by  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Bio::Factory::HitFactoryI     1.5.2    1.6    Superseded by  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Bio::Graph                    1.5.2    1.6    Superseded by bioperl- 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Bio::Tools::RNAMotif          1.5.2    1.7    Superseded by  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Bio::Tools::Infernal          1.5.2    1.7    Superseded by  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Bio::Tools::ERPIN             1.5.2    1.7    Superseded by  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