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::Seqis for Sequences (protein and DNA).
Bio::PrimarySeqis a plain sequence (sequence data + identifiers)
Bio::Seqis a fancier
PrimarySeq, in that it has annotation (via
Bio::Annotation::Collection) and sequence features (via
Bio::SeqFeatureIobjects, attached via
Bio::Seq::RichSeqis all of the above, plus it has slots for extra information specific to GenBank/EMBL/SwissProt files.
Bio::Seq::LargeSeqis for sequences which are too big for fitting into memory.
Bio::SeqIOis for reading and writing Sequences. It is a front end module for separate driver modules supporting the different sequence formats.
Bio::SeqFeaturerepresent start/stop/strand-based localised annotations (features) of sequences
Bio::SeqFeature::Genericis basic catchall
Bio::SeqFeature::Similaritya similarity sequence feature
Bio::SeqFeature::FeaturePaira sequence feature which is pairwise such as query/hit pairs
Bio::SearchIOis for reading and writing pairwise alignment reports, like BLAST or FASTA.
Bio::Searchis where the alignment objects for
Bio::Search::Result::GenericResultis the result object (a blast query is a
Hitobject (a query will have 0 to many hits in a database)
Bio::Search::HSP::GenericHSPis the High-scoring Segment Pair object defining the alignment(s) of the query and hit.
Bio::SimpleAlignis for multiple sequence alignments
Bio::AlignIOis for reading and writing multiple sequence alignment formats
Bio::Assemblyprovides the start of an infrastructure for assemblies and
Bio::Assembly::IOIO converters for them
Bio::DBis the namespace for database query classes
Bio::DB::GenBank/GenPeptare two modules which query NCBI entrez for sequences.
Bio::DB::SwissProt/EMBLquery various EMBL and SwissProt repositories for a sequences.
Bio::DB::GFFis Lincoln Stein's fast, lightweight feature and sequence database which is the backend to his GBrowse system.
Bio::DB::Flatis 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/DBFetchfor 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::Registryinterface to the OBDA specification for remote data sources.
Bio::DB::Bibliofor access to remote bibliographic databases.
Bio::DB::EUtilitiesis the initial set of modules used for generic queried using NCBI's eUtils.
Bio::Annotationcollection 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::Indexis for locally indexed flatfiles with BerkeleyDB
Bio::Toolscontains 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::Maprepresents genetic and physical map representations
Bio::Structureparse and represent protein structure data
Bio::TreeIOis for reading and writing Tree formats
Bio::Treeis the namespace for all associated Tree classes
Bio::Tree::Treeis the basic tree object
Bio::Tree::Nodeare the nodes which make up the tree
Bio::Tree::Statisticsis for computing statistics for a tree
Bio::Tree::TreeFunctionsIis where specific tree functions are implemented (like
Bio::Bibliois where bibliographic data and database access objects are kept
Bio::Variationrepresent sequences with mutations and variations applied so one can compare and represent wild-type and mutation versions of a sequence.
Bio::Rootare basic objects for the internals of BioPerl
BioPerl currently uses a semantic versioning
scheme for version numbers. Basically, a version has three numbers in
MAJOR.MINOR.PATH, each of which changes when:
MAJOR--- incompatible API changes,
MINOR--- new functionality in a backwards-compatible manner,
PATCH--- backwards-compatible bug fixes.
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).