Proposed BioPerl changes

Overview

Stemming from Chris Fields' proposal on the mailing list, this page is for tracking and determining the division of the existing bioperl (post-1.6) modules into smaller more independent distributions.

The original plan, in order to start the process, was to have a new core of well-developed and actively maintained modules, a bioperl-tools collection, a bioperl-dev grouping of experimental or otherwise less-developed modules, and a section for deprecated modules which are being phased out. A more radical restructuring is being discussed and planned, however, as of July 2009. Therefore, the contents here will very likely change dramatically over time.

core

• Bio::AnalysisI
  • Implemented by Bio::SimpleAnalysisI, which is used by many Bio::Tools modules. Could possibly be combined with Bio::SimpleAnalysisI
• Bio::AnalysisParserI
  • Implemented by Bio::SearchIO, Bio::Tools::Phylo::PAML.
• Bio::AnalysisResultI
  • Implemented by Bio::Search::Result::ResultI, Bio::Tools::Phylo::PAML::Result.
• Bio::Align
• Bio::AlignIO
• Bio::AnnotatableI
• Bio::Annotation
• Bio::AnnotationCollectionI
• Bio::AnnotationI
• Bio::Cluster
• Bio::ClusterIO
• Bio::CodonUsage
• Bio::Coordinate
• Bio::Coordinate::Result
• Bio::DBLinkContainerI
  • Implemented by Bio::Variation::VariantI, Bio::Variation::Allele
• Bio::DescribableI
• Bio::Event
• Bio::Factory
• Bio::FeatureHolderI
• Bio::Das
• Bio::DasI
• Bio::DB
• Bio::DB::Biblio
  • May need to move to bioperl-dev along with Bio::Biblio modules
• Bio::DB::Expression
• Bio::DB::EUtilities
• Bio::DB::EUtilParameters
• Bio::DB::Flat
• Bio::DB::Flat::BDB
• Bio::DB::GFF
• Bio::DB::GFF::Adaptor
• Bio::DB::GFF::Adaptor::berkeleydb
• Bio::DB::GFF::Adaptor::dbi
• Bio::DB::GFF::Adaptor::memory
• Bio::DB::GFF::Aggregator
• Bio::DB::GFF::Util
• Bio::DB::Query
• Bio::DB::SeqFeature
• Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::DBI
• Bio::DB::SeqVersion
• Bio::DB::Taxonomy
• Bio::Graphics
• Bio::Graphics::FeatureFile
• Bio::Graphics::Glyph
• Bio::HandlerBaseI
• Bio::IdentifiableI
• Bio::Index
• Bio::LiveSeq
• Bio::LiveSeq::IO
• Bio::LocatableSeq
• Bio::Location
• Bio::LocationI
• Bio::Map
• Bio::MapIO
• Bio::Matrix
• Bio::Matrix::IO
• Bio::Matrix::PSM
• Bio::Matrix::PSM::IO
• Bio::MolEvol
• Bio::Ontology
• Bio::Ontology::SimpleGOEngine
• Bio::OntologyIO
• Bio::OntologyIO::Handlers
• Bio::ParameterBaseI
• Bio::Perl
• Bio::PopGen
• Bio::PopGen::IO
• Bio::PopGen::Simulation
• Bio::PrimarySeqI
• Bio::PrimarySeq
• Bio::PullParserI
• Bio::RangeI
• Bio::Range
• Bio::Root
• Bio::Search
• Bio::Search::HSP
• Bio::Search::Hit
• Bio::Search::Iteration
• Bio::Search::Result
• Bio::SearchIO
• Bio::SearchIO::Writer
• Bio::SearchIO::XML
• Bio::Seq
• Bio::Seq::Meta
• Bio::SeqAnalysisParserI
• Bio::SeqEvolution
• Bio::SeqFeature
• Bio::SeqFeature::Gene
• Bio::SeqFeature::SiRNA
• Bio::SeqFeature::Tools
• Bio::SeqFeatureI
• Bio::SeqI
• Bio::SeqIO
• Bio::SeqIO::Handler
• Bio::SeqIO::game
• Bio::SeqIO::tinyseq
• Bio::SeqUtils
• Bio::SimpleAlign
• Bio::SimpleAnalysisI
  • Used by many Bio::Tools modules. Could possibly be combined with Bio::SimpleAnalysisI
• Bio::Species
  • to be removed after 1.6 is released, in 1.7 series (moving to Bio::Taxon only)
• Bio::Structure
• Bio::Structure::IO
• Bio::Structure::SecStr
• Bio::Structure::SecStr::DSSP
• Bio::Structure::SecStr::STRIDE
• Bio::Taxon
• Bio::Tools
  • should many of these go into bioperl-tools?
• Bio::Tools::Analysis
• Bio::Tools::Analysis::DNA
• Bio::Tools::Analysis::Protein
• Bio::Tools::EUtilities
• Bio::Tools::EUtilities::Info
• Bio::Tools::EUtilities::Link
• Bio::Tools::EUtilities::Query
• Bio::Tools::EUtilities::Summary
• Bio::Tools::Phylo
• Bio::Tools::Phylo::Molphy
• Bio::Tools::Phylo::PAML
• Bio::Tools::Phylo::Phylip
• Bio::Tools::Run
• Bio::Tools::Signalp
• Bio::Tools::Spidey
• Bio::Tree
• Bio::Tree::Draw
• Bio::TreeIO
• Bio::Variation
• Bio::Variation::IO
• Bio::WebAgent

bioperl-tools

• Bio::Biblio
  • Bio::Biblio-related classes may need reimplementation/documentation; could be redundant with Bio::Annotation::Reference (or vice versa)
• Bio::Biblio::IO
• Bio::DB::XEMBL
  • May need reimplementation as a SOAP-based service for DBFetch
• Bio::DB::XEMBLService
  • May need reimplementation as a SOAP-based service for DBFetch
• Bio::Expression
• Bio::Expression::FeatureGroup
• Bio::Expression::FeatureSet
• Bio::Microarray
• Bio::Microarray::Tools
• Bio::Phenotype
• Bio::Phenotype::MeSH
• Bio::Phenotype::OMIM
• Bio::Restriction
  • Bio::Restriction-related classes may need reimplementation/documention
• Bio::Restriction::Enzyme
• Bio::Restriction::IO
• Bio::SearchDist
  • Relies on bioperl-ext modules which haven't been maintained and seem to be giving unreliable results (Issue #1857). I believe it should be reimplemented.
• Bio::Symbol
  • I believe Jason mentioned this could be deprecated. No other modules use it. --Chris Fields 11:46, 13 February 2008 (EST)
• Bio::Taxonomy
  • Redundant with recent Species-related changes by Sendu. To be removed in 1.7 acc. to DEPRECATED
• Bio::Tools::Alignment::Consed
  • Doesn't appear to be maintained anymore in favor of Bio::Assembly
• Bio::Tools::Alignment::Trim
  • Has a note from Chad Matsalla to rewrite.
• Bio::Tools::BPlite
  • Remove in 1.6, according to DEPRECATED file
• Bio::Tools::EMBOSS
  • Only one parser.
• Bio::Tools::ERPIN
  • deprecated in favor of Bio::SearchIO::erpin
• Bio::Tools::HMMER
  • deprecated in favor of Bio::SearchIO::hmmer or Bio::SearchIO::hmm_pull
• Bio::Tools::Infernal
  • deprecated in favor of Bio::SearchIO::infernal
• Bio::Tools::Prediction
• Bio::Tools::Primer
• Bio::Tools::Primer::Assessor
• Bio::Tools::RNAMotif
  • deprecated in favor of Bio::SearchIO::rnamotif
• Bio::Tools::SiRNA
• Bio::Tools::SiRNA::Ruleset
• Bio::Tools::Sim4

Unimplemented interfaces

• Bio::UpdateableSeqI
• Bio::IdCollectionI

bioperl-dev

In-development modules (API may not be stable)

• Bio::Assembly
  • Bio::Assembly-related classes may need reimplementation
• Bio::Assembly::IO
• Bio::FeatureIO
  • May need reimplementation
• Bio::SeqFeature::Anntotated
  • May need reimplementation
• Bio::PhyloNetwork
  • Has been added very recently, not clear who will be the maintainer

deprecated for 1.6

• Bio::Factory::HitFactoryI
  • Remove in 1.6, according to DEPRECATED file
• Bio::Factory::ResultFactoryI
  • Remove in 1.6, according to DEPRECATED file
• Bio::Graph
  • Remove in 1.6, according to DEPRECATED file
• Bio::Graph::IO
  • Remove in 1.6, according to DEPRECATED file
• Bio::Graph::SimpleGraph
  • Remove in 1.6, according to DEPRECATED file