Deprecated modules

This is the Boot Hill for BioPerl modules. Rest In Peace.

See also the DEPRECATED document included with the BioPerl distribution.

Deprecation Schedule

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::Annotation	1.0	-	1.1	use Bio::Annotation::Collection
Bio::Tools::Blast	1.0	-	1.1	use Bio::SearchIO
Bio::Tools::Blast::HSP	1.0	-	1.1	use Bio::Search::HSP::GenericHSP
Bio::Tools::Blast::Sbjct	1.0	-	1.1	use Bio::Search::Hit::GenericHit
Bio::Tools::Blast::HTML	1.0	-	1.1	use Bio::SearchIO::Writer::HTMLWriter
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::UnivAln	1.0	-	1.1	use Bio::SimpleAlign
Bio::Tools::RestrictionEnzyme	1.5	1.5.2	1.6	use Bio::Restriction
Bio::Tools::BPlite	1.5	1.5.2	1.6	use Bio::SearchIO
Bio::Tools::BPpsilite	1.5	1.5.2	1.6	use Bio::SearchIO
Bio::Tools::BPbl2seq	1.5	1.5.2	1.6	use Bio::SearchIO
Bio::Ontology::SimpleGOEngine	1.5.1	1.6?	1.6	use Bio::Ontology::OBOEngine
Bio::Taxonomy	1.5.2	1.6	1.7	use Bio::Taxon & Bio::Tree::Tree
Bio::Taxonomy::Node	1.5.2	1.6	1.7	renamed Bio::Taxon
Bio::Taxonomy::Taxon	1.5.2	1.6	1.7	use Bio::Taxon
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Bio::Search::Processor	1.5.2	1.5.2	1.5.3	Superseded by Bio::SearchIO
Bio::Factory::ResultFactoryI	1.5.2	1.5.2	1.6	Superseded by Bio::Factory::ObjectFactory
Bio::Factory::HitFactoryI	1.5.2	1.5.2	1.6	Superseded by Bio::Factory::ObjectFactory
Bio::Graph	1.5.2	1.5.3	1.6	Superseded by bioperl-network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.

Bio::UnivAln

Use Bio::SimpleAlign

Bio::Annotation

Use Bio::Annotation::Collection.

Bio::Tools::Blast

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

Bio::Tools::WWW

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.

Bio::Tools::BPlite

Use Bio::SearchIO

Bio::Tools::RestrictionEnzyme

Use the various Bio::Restriction classes instead.

Bio::Taxonomy

This includes Bio::Taxonomy::Node, Bio::Taxonomy::Tree, Bio::Taxonomy::Taxon, and Bio::Taxonomy::FactoryI. Use Bio::Taxon in combination with Bio::Tree::Tree.

Bio::Species

Maintained for backwards compatibility only; gradually shifting to Bio::Taxon integration. Use Bio::Taxon instead.

Bio::Ontology::SimpleGOEngine

Use Bio::Ontology::OBOEngine

Bio::Factory::ResultFactoryI, Bio::Factory::HitFactoryI

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!

Bio::Graph modules

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.

• Bio::Graph::SimpleGraph
• Bio::Graph::ProteinGraph
• Bio::Graph::IO
• Bio::Graph::Edge

We are currently awaiting final word from Nat Goodman before marking for deprecation.

Bio::SeqIO::game

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:

http://bioperl.org/pipermail/bioperl-l/2006-August/022738.html

http://bioperl.org/pipermail/bioperl-l/2006-August/022739.html

Bio::Search::Processor

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:

http://bioperl.org/pipermail/bioperl-l/2001-January/004854.html

http://bioperl.org/pipermail/bioperl-l/2006-September/023317.html

http://bioperl.org/pipermail/bioperl-l/2006-September/023287.html

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.

An experiment

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)

• Bio::Root::Err
• Bio::Root::Global
• Bio::Root::IOManager
• Bio::Root::Object
• Bio::Root::Storable
• Bio::Root::Utilities
• Bio::Root::Vector
• Bio::Root::Xref
• t/Root-Utilities.t
• t/RootStorable.t

Will Spooner's response about Bio::Root::Storable

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/12792/focus=12855

 > 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

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/14350

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

Bio::DB::XEMBL, Bio::DB::XEMBLService

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?