- Released by
- AJPAGE
- Version
- Release Date
- 2015-05-21
- Kwalitee
- 140.62
- Core Kwalitee
- 90.62
- LINKS
Bio-Roary 2.2.2 Deleted
Kwalitee Issues
This is not the latest release. The following issues may have already been fixed in the newer releases.
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- 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::Roary::Exceptions - 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.
- 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::Roary::Exceptions
- 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.
- has_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Roary | Create a pan genome | metacpan | |
| Bio::Roary::AnalyseGroups | Take in a groups file and the original FASTA files and create plots and stats | metacpan | |
| Bio::Roary::AnnotateGroups | Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name | metacpan | |
| Bio::Roary::ChunkFastaFile | Take in a FASTA file and chunk it up into smaller pieces. | metacpan | |
| Bio::Roary::ClustersRole | A role to read a clusters file from CD hit | metacpan | |
| Bio::Roary::CombinedProteome | Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's | metacpan | |
| Bio::Roary::CommandLine::Common | Common command line settings | metacpan | |
| Bio::Roary::CommandLine::CreatePanGenome | Take in FASTA files of proteins and cluster them | metacpan | |
| Bio::Roary::CommandLine::ExtractProteomeFromGff | Take in GFF files and output the proteome | metacpan | |
| Bio::Roary::CommandLine::IterativeCdhit | Iteratively run cdhit | metacpan | |
| Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp | Take in a FASTA file of proteins and blast against itself | metacpan | |
| Bio::Roary::CommandLine::ProteinMuscleAlignmentFromNucleotides | Take in a multifasta file of nucleotides, convert to proteins and align with muscle | metacpan | |
| Bio::Roary::CommandLine::QueryRoary | Take in a groups file and the protein fasta files and output selected data | metacpan | |
| Bio::Roary::CommandLine::Roary | Take in FASTA files of proteins and cluster them | metacpan | |
| Bio::Roary::CommandLine::RoaryCoreAlignment | Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment. | metacpan | |
| Bio::Roary::CommandLine::RoaryPostAnalysis | Perform the post analysis on the pan genome | metacpan | |
| Bio::Roary::CommandLine::RoaryReorderSpreadsheet | Take in a tree and a spreadsheet and output a reordered spreadsheet | metacpan | |
| Bio::Roary::CommandLine::TransferAnnotationToGroups | Take in a groups file and a set of GFF files and transfer the consensus annotation | metacpan | |
| Bio::Roary::ContigsToGeneIDsFromGFF | Parse a GFF and efficiently and extract ordered gene ids on each contig | metacpan | |
| Bio::Roary::Exceptions | Exceptions for input data | metacpan | |
| Bio::Roary::External::Blastp | Wrapper around NCBIs blastp command | metacpan | |
| Bio::Roary::External::Cdhit | Wrapper to run cd-hit | metacpan | |
| Bio::Roary::External::IterativeCdhit | Iteratively run CDhit | metacpan | |
| Bio::Roary::External::Makeblastdb | Wrapper around NCBIs makeblastdb command | metacpan | |
| Bio::Roary::External::Mcl | Wrapper around MCL which takes in blast results and outputs clustered results | metacpan | |
| Bio::Roary::External::Muscle | Wrapper around Muscle for sequence alignment | metacpan | |
| Bio::Roary::External::PostAnalysis | Perform the post analysis | metacpan | |
| Bio::Roary::External::ProteinMuscleAlignmentFromNucleotides | Take in a multifasta file of nucleotides, convert to proteins and align with muscle | metacpan | |
| Bio::Roary::External::Revtrans | Wrapper around RevTrans | metacpan | |
| Bio::Roary::External::Segmasker | Wrapper around Segmasker for low complexity filtering | metacpan | |
| Bio::Roary::ExtractCoreGenesFromSpreadsheet | Take in a spreadsheet produced by the pipeline and identify the core genes. | metacpan | |
| Bio::Roary::ExtractProteomeFromGFF | Take in a GFF file and create protein sequences in FASTA format | metacpan | |
| Bio::Roary::ExtractProteomeFromGFFs | Take in GFF files and create protein sequences in FASTA format | metacpan | |
| Bio::Roary::FilterFullClusters | Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters | metacpan | |
| Bio::Roary::FilterUnknownsFromFasta | Take in fasta files, remove sequences with too many unknowns and return a list of the new files | metacpan | |
| Bio::Roary::GeneNamesFromGFF | Parse a GFF and efficiently extract ID -> Gene Name | metacpan | |
| Bio::Roary::GroupLabels | Add labels to the groups | metacpan | |
| Bio::Roary::GroupStatistics | Add labels to the groups | metacpan | |
| Bio::Roary::InflateClusters | Take the clusters file from cd-hit and use it to inflate the output of MCL | metacpan | |
| Bio::Roary::IterativeCdhit | Run CDhit iteratively with reducing thresholds, removing full clusters each time | metacpan | |
| Bio::Roary::JobRunner::Local | Execute a set of commands locally | metacpan | |
| Bio::Roary::JobRunner::Parallel | Use GNU Parallel | metacpan | |
| Bio::Roary::JobRunner::Role | A role to add job runner functionality | metacpan | |
| Bio::Roary::LookupGeneFiles | Take in an ordering of genes and a directory and return an ordered list of file locations | metacpan | |
| Bio::Roary::MergeMultifastaAlignments | Merge multifasta alignment files with equal numbers of sequences. | metacpan | |
| Bio::Roary::OrderGenes | Take in GFF files and create a matrix of what genes are beside what other genes | metacpan | |
| Bio::Roary::Output::BlastIdentityFrequency | Take in blast results and find the percentage identity graph | metacpan | |
| Bio::Roary::Output::DifferenceBetweenSets | Given two sets of isolates and a group file, output whats unique in each and whats in common | metacpan | |
| Bio::Roary::Output::EmblGroups | Create a tab/embl file with the features for drawing pretty pictures | metacpan | |
| Bio::Roary::Output::GroupMultifasta | Take in a group and create a multifasta file | metacpan | |
| Bio::Roary::Output::GroupsMultifastaNucleotide | Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. | metacpan | |
| Bio::Roary::Output::GroupsMultifastaProtein | Take a multifasta nucleotide file and output it as proteins. | metacpan | |
| Bio::Roary::Output::GroupsMultifastas | Take in a list of groups and create multifastas files for each group | metacpan | |
| Bio::Roary::Output::GroupsMultifastasNucleotide | Take in a set of GFF files and a groups file and output one multifasta file per group with nucleotide sequences. | metacpan | |
| Bio::Roary::Output::NumberOfGroups | Create raw output files of group counts for turning into plots | metacpan | |
| Bio::Roary::Output::QueryGroups | Output the groups of the union of a set of input isolates | metacpan | |
| Bio::Roary::ParallelAllAgainstAllBlast | Run all against all blast in parallel | metacpan | |
| Bio::Roary::ParseGFFAnnotationRole | A role for parsing a gff file efficiently | metacpan | |
| Bio::Roary::PostAnalysis | Post analysis of pan genomes | metacpan | |
| Bio::Roary::PrepareInputFiles | Take in a mixture of FASTA and GFF input files and output FASTA proteomes only | metacpan | |
| Bio::Roary::QC::Report | generate a report based on kraken output | metacpan | |
| Bio::Roary::ReorderSpreadsheet | Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns | metacpan | |
| Bio::Roary::SampleOrder | Take in a tree file and return an ordering of the samples | metacpan | |
| Bio::Roary::SequenceLengths | Take in a fasta file and create a hash with the length of each sequence | metacpan | |
| Bio::Roary::SortFasta | sort a fasta file by name | metacpan | |
| Bio::Roary::SplitGroups | metacpan |
Other Files
| MANIFEST | metacpan |
| META.yml | metacpan |
| Makefile.PL | metacpan |
| README | metacpan |
| README.md | metacpan |
| dist.ini | metacpan |