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Working with development sources

BioPerl uses Dist::Zilla to author releases. You will also need the Dist::Zilla::PluginBundle::BioPerl installed as well as its dependencies. Then, you can run the following commands:

dzil test
dzil install

The Directory Structure

The bioperl-live repository structure is organized as follows:

  • lib/ - BioPerl modules

  • examples/ - Scripts demonstrating the many uses of BioPerl

  • scripts/ - Useful production-quality scripts with POD documentation

  • t/ - Perl built-in tests, tests are divided into subdirectories based on the specific classes being tested

  • t/data/ - Data files used for the tests, provides good example data

  • travis_scripts/ - script to customize Travis

Bio:: namespace summary

The BioPerl project is split over multiple Perl module distributions. The BioPerl distribution is the BioPerl core distribution, including a selection of modules and namespaces but not all. For example, the entire Bio::Biblio is not included in the BioPerl distribution. Similarly, while many Bio::SearchIO modules in the BioPerl distribution, there also Bio::SearchIO modules in other distributions such as Bio-SearchIO-blastxml.

This section describes most of the Bio:: namespaces developed by the BioPerl project, including those which are not part of the BioPerl distribution. For example, the Bio::Biblio and Bio::Assembly are documented here but are not part of the BioPerl distribution.

  • Bio::Seq is for Sequences (protein and DNA).

    • Bio::PrimarySeq is a plain sequence (sequence data + identifiers)
    • Bio::Seq is a fancier PrimarySeq, in that it has annotation (via Bio::Annotation::Collection) and sequence features (via Bio::SeqFeatureI objects, attached via Bio::FeatureHolderI).
    • Bio::Seq::RichSeq is all of the above, plus it has slots for extra information specific to GenBank/EMBL/SwissProt files.
    • Bio::Seq::LargeSeq is for sequences which are too big for fitting into memory.

  • Bio::SeqIO is for reading and writing Sequences. It is a front end module for separate driver modules supporting the different sequence formats.

  • Bio::SeqFeature represent start/stop/strand-based localised annotations (features) of sequences

    • Bio::SeqFeature::Generic is basic catchall
    • Bio::SeqFeature::Similarity a similarity sequence feature
    • Bio::SeqFeature::FeaturePair a sequence feature which is pairwise such as query/hit pairs

  • Bio::SearchIO is for reading and writing pairwise alignment reports, like BLAST or FASTA.

  • Bio::Search is where the alignment objects for SearchIO are defined

    • Bio::Search::Result::GenericResult is the result object (a blast query is a Result object)
    • Bio::Search::Hit::GenericHit is the Hit object (a query will have 0 to many hits in a database)
    • Bio::Search::HSP::GenericHSP is the High-scoring Segment Pair object defining the alignment(s) of the query and hit.

  • Bio::SimpleAlign is for multiple sequence alignments

  • Bio::AlignIO is for reading and writing multiple sequence alignment formats

  • Bio::Assembly provides the start of an infrastructure for assemblies and Bio::Assembly::IO IO converters for them

  • Bio::DB is the namespace for database query classes

    • Bio::DB::GenBank/GenPept are two modules which query NCBI entrez for sequences.
    • Bio::DB::SwissProt/EMBL query various EMBL and SwissProt repositories for a sequences.
    • Bio::DB::GFF is Lincoln Stein's fast, lightweight feature and sequence database which is the backend to his GBrowse system.
    • Bio::DB::Flat is a fast implementation of the OBDA flat-file indexing system (cross-language and cross-platform supported by O|B|F projects see http://obda.open-bio.org).
    • Bio::DB::BioFetch/DBFetch for OBDA, Web (HTTP) access to remote databases.
    • Bio::DB::InMemoryCache/FileCache (fast local caching of sequences from remote dbs to speed up your access).
    • Bio::DB::Registry interface to the OBDA specification for remote data sources.
    • Bio::DB::Biblio for access to remote bibliographic databases.
    • Bio::DB::EUtilities is the initial set of modules used for generic queried using NCBI's eUtils.

  • Bio::Annotation collection of annotation objects (comments, DBlinks, References, and misc key/value pairs)

  • Bio::Coordinate** is a system for mapping between different coordinate systems such as DNA to protein or between assemblies

  • Bio::Index is for locally indexed flatfiles with BerkeleyDB

  • Bio::Tools contains many miscellaneous parsers and functions for different bioinformatics needs such as:

    • Gene prediction parser (Genscan, MZEF, Grail, Genemark)
    • Annotation format (GFF)
    • Enumerate codon tables and valid sequences symbols (CodonTable, IUPAC)
    • Phylogenetic program parsing (PAML, Molphy, Phylip)

  • Bio::Map represents genetic and physical map representations

  • Bio::Structure parse and represent protein structure data

  • Bio::TreeIO is for reading and writing Tree formats

  • Bio::Tree is the namespace for all associated Tree classes

    • Bio::Tree::Tree is the basic tree object
    • Bio::Tree::Node are the nodes which make up the tree
    • Bio::Tree::Statistics is for computing statistics for a tree
    • Bio::Tree::TreeFunctionsI is where specific tree functions are implemented (like is_monophyletic and lca)

  • Bio::Biblio is where bibliographic data and database access objects are kept

  • Bio::Variation represent sequences with mutations and variations applied so one can compare and represent wild-type and mutation versions of a sequence.

  • Bio::Root are basic objects for the internals of BioPerl

Releases

BioPerl currently uses a semantic versioning scheme for version numbers. Basically, a version has three numbers in the form MAJOR.MINOR.PATH, each of which changes when:

  1. MAJOR --- incompatible API changes,
  2. MINOR --- new functionality in a backwards-compatible manner,
  3. PATCH --- backwards-compatible bug fixes.

1.7 releases

Before 1.7 release, the BioPerl project had a single distribution with all of BioPerl modules. During the 1.7 release series, subsets of the modules were extracted into separate distribution.

Pre 1.7 releases

From version 1.0 until 1.6, even numbers (e.g. version 1.4) indicated stable releases. Stable releases were well tested and recommended for most uses. Odd numbers (e.g. version 1.3) were development releases which one would only use if interested in the latest features. The final number (e.g. in 1.2.1) is the point or patch release. The higher the number the more bug fixes has been incorporated. In theory you can upgrade from one point or patch release to the next with no changes to your own code (for production cases, obviously check things out carefully before you switch over).