This is the plugin bundle that CJM uses. It is equivalent to: [VersionFromModule] [GatherDir] [PruneCruft] [ManifestSkip] [MetaJSON] [MetaYAML] [License] [Test::PrereqsFromMeta] [PodSyntaxTests] [PodCoverageTests] [PodLoom] data = tools/loom.pl [Make...

This plugin is the successor to Module::Build::DistVersion. It performs the following actions: 1. It opens the Changes file, and finds the first version listed. The line must begin with the version number, and everything after the version number is c...

This plugin makes sure that module version numbers are updated as necessary. In a distribution with multiple module, I like to update a module's version only when a change is made to that module. In other words, a module's version is the version of t...

• Dist::Zilla::Plugin::Metadata - Add arbitrary keys to distmeta
• Dist::Zilla::Role::ModuleInfo - Create Module::Metadata object from Dist::Zilla::File
• Dist::Zilla::Role::HashDumper - Dump selected hash keys as a string
• 6 more results from Dist-Zilla-Plugins-CJM »

This module is for manipulating data as hierarchical tag/value pairs (Structured TAGs or Simple Tree AGgreggates). These datastructures can be represented as nested arrays, which have the advantage of being native to perl. A simple example is shown b...

• stag-diff - finds the difference between two stag files

This module is for mapping between relational databases and Stag objects (Structured Tags - see Data::Stag). Stag objects can also be represented as XML. The module has two main uses: Querying This module can take the results of any SQL query and dec...

• DBIx::DBStag::Cookbook - building and querying databases from XML
• DBIx::DBStag::SQLTemplate - A Template for an SQL query
• DBIx::DBStag::Constraint

This is a module for accessing Gene Ontology data sources, e.g the GO relational database. It defines a set of methods that provide a consistent interface independent of the way the GO data is stored. For an explanation of the GO project, please visi...

• GO::Tango - Tango ANnotates GO
• GO::AppHandles::AppHandleSqlImpl
• GO::AppHandles::AppHandlePgImpl
• 3 more results from go-db-perl »

This script loads a BioSQL database with sequences. There are a number of options that have to do with where the database is and how it's accessed and the format and namespace of the input files. These are followed by any number of file names. The fi...

Software distributions released to the CPAN include a META.json or, for older distributions, META.yml, which describes the distribution, its contents, and the requirements for building and installing the distribution. The data structure stored in the...

Dist::Zilla builds distributions of code to be uploaded to the CPAN. In this respect, it is like ExtUtils::MakeMaker, Module::Build, or Module::Install. Unlike those tools, however, it is not also a system for installing code that has been downloaded...

This script will unflatten a genbank or genbank-style file of SeqFeatures into a nested hierarchy. See Bio::SeqFeature::Tools::Unflattener In a GenBank/EMBL representation, features are 'flat' - for example, there is no link between an mRNA and a CDS...

• Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser
• Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
• Bio::SeqIO::genbank - GenBank sequence input/output stream
• 7 more results from BioPerl »

What XML::Lenient is meant to parse markup languages such as HTML and XML in the knowledge that someone, somewhere, is going to break every rule in the book. It will handle malformed XML, wrongly nested HTML tags and everything else that I have throw...

Summarises an ontology...

• GO::IO::Blast - Gene Ontology Blast Reports DEPRECATED
• GO::IO::Analysis - preliminary analysis object
• GO::Handlers::owl_to_obo_text

This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces....

• FAST::Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
• FAST::Bio::SeqIO::genbank - GenBank sequence input/output stream
• FAST::Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
• 8 more results from FAST »

The grammar is influenced heavily by Tim Bunce's "mysql2ora" grammar. Here's the word from the MySQL site (http://www.mysql.com/doc/en/CREATE_TABLE.html): CREATE [TEMPORARY] TABLE [IF NOT EXISTS] tbl_name [(create_definition,...)] [table_options] [se...

An OBOParser object parses an OBO-formatted file: http://www.geneontology.org/GO.format.obo-1_4.shtml http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html...

The grammar is influenced heavily by Tim Bunce's "mysql2ora" grammar. Here's the word from the MySQL site (http://www.mysql.com/doc/en/CREATE_TABLE.html): CREATE [TEMPORARY] TABLE [IF NOT EXISTS] tbl_name [(create_definition,...)] [table_options] [se...

This plugin is a drop-in replacement for Dist::Zilla::Plugin::MetaResources for users of Git. It *automatically* provides three resource links to your distribution metadata, based on the name of the distribution and the remote URL of the Git reposito...

Runs all xt tests before release. Dies if any fail. Sets RELEASE_TESTING and AUTHOR_TESTING. If you use Dist::Zilla::Plugin::TestRelease, you should consider using Dist::Zilla::Plugin::RunExtraTests instead, which enables xt tests to run as part of "...