Kwalitee Issues

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

no_pod_errors

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

Error: Bio-MLST-Check-2.1.1534813/lib/Bio/MLST/FilterAlleles.pm -- Around line 57: Unknown directive: =headAround line 61: Unknown directive: =head

has_meta_json

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

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.

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.

Modules

Name Abstract Version View
Bio::MLST::Blast::BlastN Wrapper around NCBI BlastN 2.0011534813 metacpan
Bio::MLST::Blast::Database Wrapper around NCBIs makeblastdb command 2.0011534813 metacpan
Bio::MLST::CDC::Convert Take in a fasta file of emmST sequences and convert it into an MLST format 2.0011534813 metacpan
Bio::MLST::Check Multilocus sequence type checking using blast 2.0011534813 metacpan
Bio::MLST::CheckMultipleSpecies High throughput multilocus sequence typing (MLST) checking against several MLST databases. 2.0011534813 metacpan
Bio::MLST::CompareAlleles Get a list of matching alleles between the sequence and database 2.0011534813 metacpan
Bio::MLST::DatabaseSettings Read in an XML file of settings and return a hash with the values. 2.0011534813 metacpan
Bio::MLST::Databases List available MLST databases 2.0011534813 metacpan
Bio::MLST::Download::Database Represents a single genus-species database on a single species 2.0011534813 metacpan
Bio::MLST::Download::Databases Represents multiple databases of species 2.0011534813 metacpan
Bio::MLST::Download::Downloadable Moose Role to download everything data 2.0011534813 metacpan
Bio::MLST::FilterAlleles 2.0011534813 metacpan
Bio::MLST::NormaliseFasta Take in a Fasta file, check for invalid characters and build a corrected file if needed. 2.0011534813 metacpan
Bio::MLST::OutputFasta Take in two hashes, both containing sequence names and sequences and output fasta files. 2.0011534813 metacpan
Bio::MLST::ProcessFasta Take in a fasta file, lookup the MLST database and create relevant files. 2.0011534813 metacpan
Bio::MLST::SearchForFiles Take in a species name and get the allele and profile files. 2.0011534813 metacpan
Bio::MLST::SequenceType Take in a list of matched alleles and look up the sequence type from the profile. 2.0011534813 metacpan
Bio::MLST::Spreadsheet::File Create a file representation of the ST results for multiple fasta files. 2.0011534813 metacpan
Bio::MLST::Spreadsheet::Row Create a row representation of the ST results for a single fasta file. 2.0011534813 metacpan
Bio::MLST::Types Moose types to use for validation. 2.0011534813 metacpan
Bio::MLST::Validate::Executable Validates the executable is available in the path before running it. 2.0011534813 metacpan
Bio::MLST::Validate::File Check to see if a file exists. For validation when classes have input files. 2.0011534813 metacpan
Bio::MLST::Validate::Resource Check to see if a file exists or if a uri is valid. For validation when classes have input files which may be local or on the web. 2.0011534813 metacpan

Other Files

MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README.md metacpan
dist.ini metacpan