Section 3

Section 3 of the manual describes all library functions excluding the library functions (system call wrappers) described in Section 2, which implement system calls.

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Bio::PrimerDesigner::epcr: A class for accessing the epcr binary
Bio::PrimerDesigner::ispcr: A class for accessing the isPcr (in-silico PCR) binary
Bio::PrimerDesigner::primer3: An class for accessing primer3
Bio::Procedural: Simple low-dependency procedural interfaces to BioPerl
Bio::PullParserI: A base module for fast 'pull' parsing
Bio::Range: Pure perl RangeI implementation
Bio::RangeI: Range interface
Bio::Roary: Create a pan genome
Bio::Roary::AccessoryBinaryFasta: Output a FASTA file which represents the binary presence and absence of genes in the accessory genome
Bio::Roary::AccessoryClustering: Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters
Bio::Roary::AnalyseGroups: Take in a groups file and the original FASTA files and create plots and stats
Bio::Roary::AnnotateGroups: Take in a group file and associated GFF files for the isolates and update the group name to the gene name
Bio::Roary::AssemblyStatistics: Given a spreadsheet of gene presence and absence calculate some statistics
Bio::Roary::BedFromGFFRole: A role to create a bed file from a gff
Bio::Roary::ChunkFastaFile: Take in a FASTA file and chunk it up into smaller pieces
Bio::Roary::ClustersRole: A role to read a clusters file from CD hit
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
Bio::Roary::CommandLine::AssemblyStatistics: Given a spreadsheet of gene presence and absence calculate some statistics
Bio::Roary::CommandLine::Common: Common command line settings
Bio::Roary::CommandLine::CreatePanGenome: Take in FASTA files of proteins and cluster them
Bio::Roary::CommandLine::ExtractProteomeFromGff: Take in GFF files and output the proteome
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides: Take in a multifasta file of nucleotides, convert to proteins and align with PRANK
Bio::Roary::CommandLine::IterativeCdhit: Iteratively run cdhit
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp: Take in a FASTA file of proteins and blast against itself
Bio::Roary::CommandLine::QueryRoary: Take in a groups file and the protein fasta files and output selected data
Bio::Roary::CommandLine::Roary: Take in FASTA files of proteins and cluster them
Bio::Roary::CommandLine::RoaryCoreAlignment: Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment
Bio::Roary::CommandLine::RoaryPostAnalysis: Perform the post analysis on the pan genome
Bio::Roary::CommandLine::RoaryReorderSpreadsheet: Take in a tree and a spreadsheet and output a reordered spreadsheet
Bio::Roary::CommandLine::TransferAnnotationToGroups: Take in a groups file and a set of GFF files and transfer the consensus annotation
Bio::Roary::CommandLine::UniqueGenesPerSample: Take in the clustered file and produce a sorted file with the frequency of each samples unique genes
Bio::Roary::ContigsToGeneIDsFromGFF: Parse a GFF and efficiently and extract ordered gene ids on each contig
Bio::Roary::Exceptions: Exceptions for input data
Bio::Roary::External::Blastp: Wrapper around NCBIs blastp command
Bio::Roary::External::Cdhit: Wrapper to run cd-hit
Bio::Roary::External::CheckTools: Check external executables are available and are the correct version
Bio::Roary::External::Fasttree: Wrapper to run Fasttree
Bio::Roary::External::GeneAlignmentFromNucleotides: Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT
Bio::Roary::External::IterativeCdhit: Iteratively run CDhit
Bio::Roary::External::Mafft: Wrapper to run mafft
Bio::Roary::External::Makeblastdb: Wrapper around NCBIs makeblastdb command
Bio::Roary::External::Mcl: Wrapper around MCL which takes in blast results and outputs clustered results
Bio::Roary::External::PostAnalysis: Perform the post analysis
Bio::Roary::External::Prank: Wrapper to run prank
Bio::Roary::ExtractCoreGenesFromSpreadsheet: Take in a spreadsheet produced by the pipeline and identify the core genes
Bio::Roary::ExtractProteomeFromGFF: Take in a GFF file and create protein sequences in FASTA format
Bio::Roary::ExtractProteomeFromGFFs: Take in GFF files and create protein sequences in FASTA format
Bio::Roary::FilterFullClusters: Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters
Bio::Roary::FilterUnknownsFromFasta: Take in fasta files, remove sequences with too many unknowns and return a list of the new files
Bio::Roary::GeneNamesFromGFF: Parse a GFF and efficiently extract ID -> Gene Name
Bio::Roary::GroupLabels: Add labels to the groups
Bio::Roary::GroupStatistics: Add labels to the groups
Bio::Roary::InflateClusters: Take the clusters file from cd-hit and use it to inflate the output of MCL
Bio::Roary::IterativeCdhit: Run CDhit iteratively with reducing thresholds, removing full clusters each time
Bio::Roary::JobRunner::Local: Execute a set of commands locally
Bio::Roary::JobRunner::Parallel: Use GNU Parallel
Bio::Roary::JobRunner::Role: A role to add job runner functionality
Bio::Roary::LookupGeneFiles: Take in an ordering of genes and a directory and return an ordered list of file locations
Bio::Roary::MergeMultifastaAlignments: Merge multifasta alignment files with equal numbers of sequences
Bio::Roary::OrderGenes: Take in GFF files and create a matrix of what genes are beside what other genes
Bio::Roary::Output::BlastIdentityFrequency: Take in blast results and find the percentage identity graph
Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL: Create an embl file for the header with locations of where genes are in the multifasta alignment of core genes
Bio::Roary::Output::DifferenceBetweenSets: Given two sets of isolates and a group file, output whats unique in each and whats in common
Bio::Roary::Output::EMBLHeaderCommon: a role containing some common methods for embl header files
Bio::Roary::Output::EmblGroups: Create a tab/embl file with the features for drawing pretty pictures
Bio::Roary::Output::GroupMultifasta: Take in a group and create a multifasta file
Bio::Roary::Output::GroupsMultifastaNucleotide: Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences
Bio::Roary::Output::GroupsMultifastaProtein: Take a multifasta nucleotide file and output it as proteins
Bio::Roary::Output::GroupsMultifastas: Take in a list of groups and create multifastas files for each group
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
Bio::Roary::Output::NumberOfGroups: Create raw output files of group counts for turning into plots
Bio::Roary::Output::QueryGroups: Output the groups of the union of a set of input isolates
Bio::Roary::ParallelAllAgainstAllBlast: Run all against all blast in parallel
Bio::Roary::ParseGFFAnnotationRole: A role for parsing a gff file efficiently
Bio::Roary::PostAnalysis: Post analysis of pan genomes
Bio::Roary::PrepareInputFiles: Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
Bio::Roary::PresenceAbsenceMatrix: Create a matrix with presence and absence
Bio::Roary::QC::Report: generate a report based on kraken output
Bio::Roary::ReformatInputGFFs: Take in gff files and add suffix where a gene id is seen twice
Bio::Roary::ReorderSpreadsheet: Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns
Bio::Roary::SampleOrder: Take in a tree file and return an ordering of the samples
Bio::Roary::SequenceLengths: Take in a fasta file and create a hash with the length of each sequence
Bio::Roary::SortFasta: sort a fasta file by name
Bio::Roary::SplitGroups: split groups
Bio::Roary::SpreadsheetRole: Read and write a spreadsheet
Bio::Roary::UniqueGenesPerSample: Take in the clustered file and produce a sorted file with the frequency of each samples unique genes
Bio::Root::Exception: BioPerl exceptions
Bio::Root::HTTPget: module for fallback HTTP get operations when LWP:: is unavailable
Bio::Root::IO: BioPerl base IO handling class
Bio::Root::Root: implementation of Bio::Root::RootI interface
Bio::Root::RootI: base interface for all BioPerl classes
Bio::Root::Storable: Safely store/retrieve objects from disk
Bio::Root::Test: common base for all BioPerl test scripts
Bio::Root::TestObject: TestObject - An implementation of TestInterface
Bio::Root::Utilities: general-purpose utilities
Bio::Root::Version: don't use, get version from each module
Bio::SCF: Perl extension for reading and writing SCF sequence files
Bio::Search::BlastStatistics: An object for Blast statistics
Bio::Search::BlastUtils: Utility functions for Bio::Search:: BLAST objects
Bio::Search::DatabaseI: Interface for a database used in a sequence search