Proposed BioPerl changes

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Contents

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
  • Bio::AnalysisParserI
  • Bio::AnalysisResultI
  • 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
  • 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
  • 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
  • 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
  • Bio::Tools::HMMER
  • Bio::Tools::Infernal
  • Bio::Tools::Prediction
  • Bio::Tools::Primer
  • Bio::Tools::Primer::Assessor
  • Bio::Tools::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
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