GenOO 1.4.1-TRIAL
- Released by
- MNSMAR
- Version
- Release Date
- 2014-01-29
- Kwalitee
- 137.5
- Core Kwalitee
- 90.62
- LINKS
GenOO 1.4.1-TRIAL
Kwalitee Issues
- has_license_in_source_file
-
Add =head1 LICENSE and the text of the license to the main module in your code.
- use_strict
-
Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.
Error: GenOO::GeneCollection::Factory, GenOO::RegionCollection::Factory, GenOO::TranscriptCollection::Factory
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- meta_yml_declares_perl_version
-
If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- has_known_license_in_source_file
-
Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: GenOO::GeneCollection::Factory, GenOO::Helper::MyMath, GenOO::Module::Search::Binary, GenOO::RegionCollection::Factory, GenOO::TranscriptCollection::Factory
- meta_yml_has_provides
-
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| GenOO | A Modern Perl Framework for High Throughput Sequencing analysis | metacpan | |
| GenOO::Data::DB::Connector | metacpan | ||
| GenOO::Data::DB::DBIC::Species::Schema | Schema object | metacpan | |
| GenOO::Data::DB::DBIC::Species::Schema::Result::Draft | Draft DBIx::Class result class for a sequencing sample database table | metacpan | |
| GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v1 | DBIC Result class for sequenced reads | metacpan | |
| GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v2 | DBIC Result class for sequenced reads | metacpan | |
| GenOO::Data::File::BED | Object implementing methods for accessing bed formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1) | metacpan | |
| GenOO::Data::File::BED::Record | Object representing a record of a bed file | metacpan | |
| GenOO::Data::File::FASTA | Object implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1) | metacpan | |
| GenOO::Data::File::FASTA::Record | Object representing a record of a fasta file | metacpan | |
| GenOO::Data::File::FASTQ | Object implementing methods for accessing fastq formatted files | metacpan | |
| GenOO::Data::File::FASTQ::Record | Object representing a record of a fastq file | metacpan | |
| GenOO::Data::File::GFF | Object implementing methods for accessing GFF formatted files (http://www.sanger.ac.uk/resources/software/gff/spec.html) | metacpan | |
| GenOO::Data::File::GFF::Record | Object representing a record of a gff file | metacpan | |
| GenOO::Data::File::SAM | Object implementing methods for accessing SAM formatted files | metacpan | |
| GenOO::Data::File::SAM::Cigar | Role that corresponds to the SAM file CIGAR string | metacpan | |
| GenOO::Data::File::SAM::CigarAndMDZ | Role that combines SAM CIGAR string with MD:Z tag | metacpan | |
| GenOO::Data::File::SAM::MDZ | Role - The MD:Z tag in a SAM file | metacpan | |
| GenOO::Data::File::SAM::Record | Object representing a record of a sam file | metacpan | |
| GenOO::Data::Structure::DoubleHashArray | Object for a data structure which corresponds of a 2D hash whose values are references to array | metacpan | |
| GenOO::Exon | Exon object | metacpan | |
| GenOO::Gene | Gene object | metacpan | |
| GenOO::GeneCollection::Factory | Factory for creating L<GenOO::RegionCollection> objects | metacpan | |
| GenOO::GeneCollection::Factory::FromTranscriptCollection | Factory for creating GenOO::GeneCollection object from a Transcript Collection and a hash{transcript_name} = genename | metacpan | |
| GenOO::GenomicRegion | Object that corresponds to a region on a genome | metacpan | |
| GenOO::Helper::MyMath | A collection of useful mathematical methods | 1.0 | metacpan |
| GenOO::Intron | Intron object | metacpan | |
| GenOO::Junction | A junction (eg exon-exon) object with features | metacpan | |
| GenOO::Module::Search::Binary | Module that offers methods for searching in an array using binary search | metacpan | |
| GenOO::Region | Role that represents a region on a reference sequence | metacpan | |
| GenOO::RegionCollection | Role for a collection of GenOO::Region objects | metacpan | |
| GenOO::RegionCollection::Factory | Factory for creating L<GenOO::RegionCollection> objects | metacpan | |
| GenOO::RegionCollection::Factory::BED | Factory for creating GenOO::RegionCollection object from a BED file | metacpan | |
| GenOO::RegionCollection::Factory::DBIC | metacpan | ||
| GenOO::RegionCollection::Factory::RegionArray | Factory for creating a RegionCollection from array of regions | metacpan | |
| GenOO::RegionCollection::Factory::Requires | Role for a concrete factory that creates GenOO::RegionCollection objects | metacpan | |
| GenOO::RegionCollection::Factory::SAM | Factory for creating GenOO::RegionCollection object from a SAM file | metacpan | |
| GenOO::RegionCollection::Type::DBIC | Class for a collection of GenOO::Region objects stored in a database. | metacpan | |
| GenOO::RegionCollection::Type::DoubleHashArray | Object for a collection of GenOO::Region objects, with features | metacpan | |
| GenOO::Spliceable | Role for a region that can be spliced | metacpan | |
| GenOO::Transcript | Corresponds to a gene transcript | metacpan | |
| GenOO::Transcript::CDS | Transcript part (coding sequence) | metacpan | |
| GenOO::Transcript::Part | A functional region within a transcript consisting of spliceable elements | metacpan | |
| GenOO::Transcript::UTR3 | Transcript part (coding sequence) | metacpan | |
| GenOO::Transcript::UTR5 | metacpan | ||
| GenOO::TranscriptCollection | Role for a collection of GenOO::Transcript objects | metacpan | |
| GenOO::TranscriptCollection::Factory | Factory for creating L<GenOO::TranscriptCollection> objects | metacpan | |
| GenOO::TranscriptCollection::Factory::GTF | metacpan |