This is the Boot Hill for BioPerl modules. Rest In Peace.
This is the schedule for modules which are deprecated and later removed from the toolkit
|Deprecated Modules||Version Deprecated||Warnings Added||Version Removed||Comment|
|Bio::Tools::SeqAnal||1.0||-||1.1||used only by deprecated Bio::Tools::Blast|
|Bio::Tools::WWW||1.1||-||1.1.1||Just a collection of links|
|Bio::Taxonomy||1.5.2||1.6||1.7||use Bio::Taxon & Bio::Tree::Tree|
|Bio::Taxonomy::Tree||1.5.2||1.6||1.7||use Bio::Taxon & Bio::Tree::Tree|
|Bio::Taxonomy::FactoryI||1.5.2||1.6||1.7||Redundant, no implementors|
|Bio::Search::Processor||1.5.2||1.5.2||1.5.3||Superseded by Bio::SearchIO|
|Bio::Factory::ResultFactoryI||1.5.2||1.5.2||1.6||Superseded by Bio::Factory::ObjectFactory|
|Bio::Factory::HitFactoryI||1.5.2||1.5.2||1.6||Superseded by Bio::Factory::ObjectFactory|
|Bio::Graph||1.5.2||1.5.3||1.6||Superseded by bioperl-network|
|Bio::Root::Err||1.5.2||-||1.5.2||Bio::Root* redundant classes|
|Bio::Root::Global||1.5.2||-||1.5.2||Bio::Root* redundant classes|
|Bio::Root::IOManager||1.5.2||-||1.5.2||Bio::Root* redundant classes|
|Bio::Root::Object||1.5.2||-||1.5.2||Bio::Root* redundant classes|
|Bio::Root::Vector||1.5.2||-||1.5.2||Bio::Root* redundant classes|
|Bio::Root::Xref||1.5.2||-||1.5.2||Bio::Root* redundant classes|
|Bio::Tools::WebBlat||1.5.2||-||1.5.3||Requested that this not be maintained|
|Bio::DB::XEMBL||1.5.3||-||?||Service no longer available; use DBFetch|
|Bio::DB::XEMBLService||1.5.3||-||?||Service no longer available; use DBFetch|
Removed from distribution
These have been removed from BioPerl distribution, so no longer are a part of the most current BioPerl stable and developer distributions.
This includes Bio::Tools::Blast, Bio::Tools::Blast::HSP, Bio::Tools::Blast::Sbjct, and Bio::Tools::Blast::HTML. Use the comparable Bio::SearchIO classes instead : Bio::SearchIO, Bio::Search::HSP::GenericHSP, Bio::Search::Hit::GenericHit, Bio::SearchIO::Writer::HTMLResultWriter
A collection of links.
Deprecated (no longer maintained)
These are modules in the current stable or developer distribution, but current plans are to have them removed in the next release or so.
Use the various Bio::Restriction classes instead.
See Issue #1419. The various Bio::SearchIO handlers currently utilize a generic object factory (Bio::Factory::ObjectFactory for Results, Hits, and HSPs. No modules currently use these BLAST-specific Factory interfaces.
On the chopping block...
These are modules that are being targeted for eventual removal. If you want to save them, then now's your chance to plead for their survival!
bioperl-network has all the same functionality as the various Bio::Graph modules and more. Currently these modules are not maintained. We encourage users of the following modules to use bioperl-network instead.
We are currently awaiting final word from Nat Goodman before marking for deprecation.
The GAME XML sequence format support in Bioperl is incomplete and hasn't been updated to work with recent format changes. Furthermore there seems to be a gradual migration away from GAME XML to Chado XML, leading to the lack of maintenance for this module over the last several years. We recommend using Apollo for updated GAME XML sequence conversion. See the following links:
Torsten: > While auditing bioperl-live recently I noticed your module > Bio/Search/Processor.pm which is unreferenced anywhere else, and it > looks like a deployer module, but there is no directory > Bio/Search/Processor/ > > The last real CVS entry was > date: 2000/11/20 17:10:57; author: jason; state: Exp; lines: +10 -11 > "likely meaningless changes as we will probably chuck these modules" Aaron: I don't know that it even needs to be deprecated - no code uses it, it should just (finally) be chucked (it was the predecessor of the SearchIO engine).
Bio::Root::Object, Bio::Root::Xref, Bio::Root::Vector, Bio::Root::Err, Bio::Root::Global, Bio::Root::IOManager
Most of the above were originally marked for deprecation during the transition to using the Bio::Root::RootI interface. See the following links for more information:
Two additional modules (Bio::Root::Utilities, Bio::Root::Storable) potentially have users, though only the latter has seen any use in recent years. Bio::Root::Utilities, while not in the 1.5.2 release, has been added back per Steve Chervitz's request with additional tests; it no longer relies on the other deprecated Bio::Root modules.
As I recently removed all references to Bio::Root::Object, today I did a fresh CVS checkout of bioperl-live, and deleted the following modules and tests, and all tests passed with
BIOPERLDEBUG=0 -- Torsten 02:02, 2 October 2006 (EDT)
Will Spooner's response about Bio::Root::Storable
> The only one I worry about is Bio::Root::Storable b/c of Ensembl. > Does anyone know where Will Spooner is? He's the maintainer for > Bio::Root::Storable. > Hi Chris, I'm still lurking... If the tests for Bio::Root::Storable still pass (I assume that they do), then the module is working as advertised. The idea behind Storable is very simple; object instances of any inhereting class can be serialised/retrieved from disk. BioPerl objects will probably not want this functionality by default, but it is trival to implement if needed. Will
Steve Chervitz's response about Bio::Root::Utilities
I noticed that Bio::Root::Utilities was purged from bioperl-live for the 1.5.2 release, but I'd like us to consider adding it back. I agree that the other purged Root modules were ancient relics of the past, but Bio::Root:: Utilities.pm still has signs of life (at least I still find occasion to use it, or refer to code in it). I know that it's not currently used by any other modules in Bioperl, but there are likely some legacy scripts out there that rely on it. Probably most of those scripts are ones I've written, but there have been substantive commits by others in the not-to-distant past (Dec 2005), so at least some folks besides myself are using it and may hesitate to upgrade their bioperl installation if it's absent. I'm all for avoiding bloat in the codebase and am eager to see Bioperl be more lean and mean, but I'd like to keep this module around. I'll agree to add some tests for it as well as clean some things up (e.g., use Bio::Root::IO to get temp file name). Cheers, Steve
The XEMBL service is no longer active; most of the functionality has been taken over by DBFetch (and, presumably, Bio::DB::DBFetch). Maybe we need to update BioPerl interaction with DBFetch accordingly? Or have a SOAP::Lite-based DBFetch interface?