Kwalitee Issues

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: Bio::Gonzales::Util::Development::Module

prereq_matches_use

List all used modules in META.yml requires

Error:

  • Bio::Graphics
  • Bio::Graphics::Glyph::generic
  • Bio::Phylo::IO
  • Bio::Root::Root
  • Bio::SearchIO
  • Bio::SeqFeature::Generic
  • Bio::SeqIO
  • Color::Spectrum
  • GO::Model::Graph
  • GO::Model::GraphIterator
  • GO::Model::Relationship
  • GO::Model::Term
  • GO::Parser
  • Graph
  • Graph::Directed
  • Log::Log4perl
  • Params::Validate
  • SVG
  • Set::IntervalTree
  • YAML
  • namespace::clean

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: Bio-Gonzales-0.082/lib/Bio/Gonzales/Project/Introduction.pod -- Around line 172: '=item' outside of any '=over' Around line 195: You forgot a '=back' before '=head2' Bio-Gonzales-0.082/lib/Bio/Gonzales/SummarizedExperiment.pm -- Around line 895: Unterminated C< ... > sequence Around line 905: Unterminated C< ... > sequence Bio-Gonzales-0.082/lib/Bio/Gonzales/Util/Cerial.pm -- Around line 243: '=item' outside of any '=over' Around line 275: You forgot a '=back' before '=head1'

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

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: Bio::Gonzales::Graphics::Glyph::colorfulBox, Bio::Gonzales::Util::Development::Module

test_prereq_matches_use

List all modules used in the test suite in META.yml test_requires

Error:

  • Test::Exception
  • Test::Fatal

consistent_version

Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).

Error: 0.0101,0.082

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
Bio::Gonzales Speedy functions to manipulate biological data 0.082 metacpan
Bio::Gonzales::Align 0.082 metacpan
Bio::Gonzales::Align::ConsensePrimer 0.082 metacpan
Bio::Gonzales::Align::ConsensePrimer1 0.082 metacpan
Bio::Gonzales::Align::IO 0.082 metacpan
Bio::Gonzales::Align::IO::MAF 0.082 metacpan
Bio::Gonzales::Align::IO::Stockholm IO class for the stockholm format 0.082 metacpan
Bio::Gonzales::Align::Jalview 0.082 metacpan
Bio::Gonzales::Assembly::IO assembly related stuff 0.082 metacpan
Bio::Gonzales::Domain::Group 0.082 metacpan
Bio::Gonzales::Domain::Identification::HMMER 0.082 metacpan
Bio::Gonzales::Feat a sequence feature 0.082 metacpan
Bio::Gonzales::Feat::IO 0.082 metacpan
Bio::Gonzales::Feat::IO::BED 0.082 metacpan
Bio::Gonzales::Feat::IO::Base 0.082 metacpan
Bio::Gonzales::Feat::IO::CDhit 0.082 metacpan
Bio::Gonzales::Feat::IO::GFF3 read and write gff files 0.082 metacpan
Bio::Gonzales::Feat::IO::MUM 0.082 metacpan
Bio::Gonzales::Feat::IO::SWISS 0.082 metacpan
Bio::Gonzales::GO::Util 0.082 metacpan
Bio::Gonzales::Graphics::BLAST make your blast result nice 0.082 metacpan
Bio::Gonzales::Graphics::Glyph::colorfulBox 0.082 metacpan
Bio::Gonzales::IDMapIO remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO 0.082 metacpan
Bio::Gonzales::Matrix::IO Library for simple matrix IO 0.082 metacpan
Bio::Gonzales::Matrix::IO::csv 0.082 metacpan
Bio::Gonzales::Matrix::Util 0.082 metacpan
Bio::Gonzales::MiniFeat 0.082 metacpan
Bio::Gonzales::Phylo::Dendroscope Color phylogenetic trees in Dendroscope format 0.082 metacpan
Bio::Gonzales::Phylo::IO 0.082 metacpan
Bio::Gonzales::Phylo::Util utility functions for phylogenetic analysis 0.082 metacpan
Bio::Gonzales::PrimarySeqIX 0.082 metacpan
Bio::Gonzales::Project 0.082 metacpan
Bio::Gonzales::Project::Functions organize your computational experiments 0.082 metacpan
Bio::Gonzales::Range::Cluster cluster sorted ranges iteratively 0.082 metacpan
Bio::Gonzales::Range::GroupedOverlap cluster overlapping ranges that are in the same group 0.082 metacpan
Bio::Gonzales::Range::Overlap find overlapping ranges 0.082 metacpan
Bio::Gonzales::Range::Util 0.082 metacpan
Bio::Gonzales::Role::BioPerl::Constructor 0.082 metacpan
Bio::Gonzales::Search::IO::BLAST 0.082 metacpan
Bio::Gonzales::Search::IO::HMMER3 0.082 metacpan
Bio::Gonzales::Seq Gonzales Sequence Object 0.082 metacpan
Bio::Gonzales::Seq::Filter filter sequence data 0.082 metacpan
Bio::Gonzales::Seq::Filter::DuplicateSeqs 0.082 metacpan
Bio::Gonzales::Seq::Filter::ProteinCleaner clean protein sequences 0.082 metacpan
Bio::Gonzales::Seq::IO fast utility functions for sequence IO 0.082 metacpan
Bio::Gonzales::Seq::IO::Fasta 0.082 metacpan
Bio::Gonzales::Seq::IO::fastq 0.082 metacpan
Bio::Gonzales::Seq::LongestTranscript 0.082 metacpan
Bio::Gonzales::Seq::Util 0.082 metacpan
Bio::Gonzales::Seq::Validate::fasta 0.082 metacpan
Bio::Gonzales::Stat::Util 0.082 metacpan
Bio::Gonzales::String::Util 0.0101 metacpan
Bio::Gonzales::SummarizedExperiment represent experimental matrix-like data (assay) with features and sample info 0.0101 metacpan
Bio::Gonzales::Tools::SeqMask 0.082 metacpan
Bio::Gonzales::Tools::SeqStats 0.082 metacpan
Bio::Gonzales::Util Utility functions for common tasks 0.082 metacpan
Bio::Gonzales::Util::Cerial convenience functions for yaml and json IO 0.082 metacpan
Bio::Gonzales::Util::Development functions handy for general development 0.082 metacpan
Bio::Gonzales::Util::Development::File Helper functions for all filesystem related tasks 0.082 metacpan
Bio::Gonzales::Util::Development::Module functions handy for module development 0.082 metacpan
Bio::Gonzales::Util::File Utility functions for file stuff 0.082 metacpan
Bio::Gonzales::Util::Graphics::Color::Generator 0.082 metacpan
Bio::Gonzales::Util::IO::Compressed metacpan
Bio::Gonzales::Util::Log basic logging for Bio::Gonzales 0.082 metacpan
Bio::Gonzales::Util::Math 0.082 metacpan
Bio::Gonzales::Util::Math::kNN::via::Distances Calculate kNN clusterings from already calculated distances 0.082 metacpan
Bio::Gonzales::Util::Role::FileIO 0.082 metacpan
Bio::Gonzales::Util::Text text and string functions 0.082 metacpan
Bio::Gonzales::Var::IO::VCF parse VCF files 0.0101 metacpan
Bio::Gonzales::Var::Util 0.0101 metacpan

Provides

Name File View
Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER::SeqMarks lib/Bio/Gonzales/Domain/Identification/HMMER/SeqMarks.pm metacpan
Bio::Matrix::IO::mcl lib/Bio/Gonzales/Matrix/IO/mcl.pm metacpan

Other Files

Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.yml metacpan
README metacpan
dist.ini metacpan