Bio-PanGenome 1.133090
- Released by
- AJPAGE
- Version
- Release Date
- 2013-11-06
- Kwalitee
- 140.62
- Core Kwalitee
- 90.62
- LINKS
Bio-PanGenome 1.133090 Deleted
Kwalitee Issues
- 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::PanGenome::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::PanGenome::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::PanGenome | Create a pan genome | metacpan | |
| Bio::PanGenome::AnalyseGroups | Take in a groups file and the original FASTA files and create plots and stats | metacpan | |
| Bio::PanGenome::AnnotateGroups | Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name | metacpan | |
| Bio::PanGenome::ChunkFastaFile | Take in a FASTA file and chunk it up into smaller pieces. | metacpan | |
| Bio::PanGenome::ClustersRole | A role to read a clusters file from CD hit | metacpan | |
| Bio::PanGenome::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::PanGenome::CommandLine::CreatePanGenome | Take in FASTA files of proteins and cluster them | metacpan | |
| Bio::PanGenome::CommandLine::ExtractProteomeFromGff | Take in GFF files and output the proteome | metacpan | |
| Bio::PanGenome::CommandLine::PanGenomePostAnalysis | Perform the post analysis on the pan genome | metacpan | |
| Bio::PanGenome::CommandLine::PanGenomeReorderSpreadsheet | Take in a tree and a spreadsheet and output a reordered spreadsheet | metacpan | |
| Bio::PanGenome::CommandLine::ParallelAllAgainstAllBlastp | Take in a FASTA file of proteins and blast against itself | metacpan | |
| Bio::PanGenome::CommandLine::PlotPanGenomeGroups | Take in the groups file and output some summary plots | metacpan | |
| Bio::PanGenome::CommandLine::QueryPanGenome | Take in a groups file and the protein fasta files and output selected data | metacpan | |
| Bio::PanGenome::CommandLine::TransferAnnotationToGroups | Take in a groups file and a set of GFF files and transfer the consensus annotation | metacpan | |
| Bio::PanGenome::Exceptions | Exceptions for input data | metacpan | |
| Bio::PanGenome::External::Blastp | Wrapper around NCBIs blastp command | metacpan | |
| Bio::PanGenome::External::Cdhit | Wrapper to run cd-hit | metacpan | |
| Bio::PanGenome::External::Makeblastdb | Wrapper around NCBIs makeblastdb command | metacpan | |
| Bio::PanGenome::External::Mcl | Wrapper around MCL which takes in blast results and outputs clustered results | metacpan | |
| Bio::PanGenome::External::Muscle | Wrapper around Muscle for sequence alignment | metacpan | |
| Bio::PanGenome::External::PostAnalysis | Perform the post analysis | metacpan | |
| Bio::PanGenome::External::Segmasker | Wrapper around Segmasker for low complexity filtering | metacpan | |
| Bio::PanGenome::ExtractProteomeFromGFF | Take in a GFF file and create protein sequences in FASTA format | metacpan | |
| Bio::PanGenome::ExtractProteomeFromGFFs | Take in GFF files and create protein sequences in FASTA format | metacpan | |
| Bio::PanGenome::FilterFullClusters | Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters | metacpan | |
| Bio::PanGenome::FilterUnknownsFromFasta | Take in fasta files, remove sequences with too many unknowns and return a list of the new files | metacpan | |
| Bio::PanGenome::GeneNamesFromGFF | Parse a GFF and efficiently extract ID -> Gene Name | metacpan | |
| Bio::PanGenome::GroupLabels | Add labels to the groups | metacpan | |
| Bio::PanGenome::GroupStatistics | Add labels to the groups | metacpan | |
| Bio::PanGenome::InflateClusters | Take the clusters file from cd-hit and use it to inflate the output of MCL | metacpan | |
| Bio::PanGenome::JobRunner::LSF | Execute a set of commands using LSF | metacpan | |
| Bio::PanGenome::JobRunner::Local | Execute a set of commands locally | metacpan | |
| Bio::PanGenome::JobRunner::Role | A role to add job runner functionality | metacpan | |
| Bio::PanGenome::Output::DifferenceBetweenSets | Given two sets of isolates and a group file, output whats unique in each and whats in common | metacpan | |
| Bio::PanGenome::Output::GroupMultifasta | Take in a group and create a multifasta file | metacpan | |
| Bio::PanGenome::Output::GroupTabFiles | Take in an array of files and output raw tab files for analysis by R to turn into plots | metacpan | |
| Bio::PanGenome::Output::GroupsMultifastaNucleotide | Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. | metacpan | |
| Bio::PanGenome::Output::GroupsMultifastas | Take in a list of groups and create multifastas files for each group | metacpan | |
| Bio::PanGenome::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::PanGenome::Output::NumberOfGroups | Create raw output files of group counts for turning into plots | metacpan | |
| Bio::PanGenome::Output::OneGenePerGroupFasta | Output a fasta file with one gene per group | metacpan | |
| Bio::PanGenome::Output::QueryGroups | Output the groups of the union of a set of input isolates | metacpan | |
| Bio::PanGenome::ParallelAllAgainstAllBlast | Run all against all blast in parallel | metacpan | |
| Bio::PanGenome::Plot::FreqOfGenes | Take in an array of frequencies of groups and output a plot | metacpan | |
| Bio::PanGenome::PostAnalysis | Post analysis of pan genomes | metacpan | |
| Bio::PanGenome::PrepareInputFiles | Take in a mixture of FASTA and GFF input files and output FASTA proteomes only | metacpan | |
| Bio::PanGenome::ReorderSpreadsheet | Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns | metacpan | |
| Bio::PanGenome::SampleOrder | Take in a tree file and return an ordering of the samples | metacpan | |
| Bio::PanGenome::SequenceLengths | Take in a fasta file and create a hash with the length of each sequence | metacpan |