section 3 · Library functions 📚

B (continued)

• Bio::MAGE::Protocol::Parameter(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::Parameterizable(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::ParameterizableApplication(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::ParameterValue(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::Protocol(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::ProtocolApplication(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::Software(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::Protocol::SoftwareApplication(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType(3pm)Container module for classes in the MAGE package: QuantitationType✨
• Bio::MAGE::QuantitationType::ConfidenceIndicator(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::DerivedSignal(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::Error(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::ExpectedValue(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::Failed(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::MeasuredSignal(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::PresentAbsent(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::PValue(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::QuantitationType(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::Ratio(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::SpecializedQuantitationType(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::QuantitationType::StandardQuantitationType(3pm)Class for the MAGE-OM API✨
• Bio::MAGE::SQLUtils(3pm)a module for exporting MAGE-OM objects to a database✨
• Bio::MAGE::Tools::MGEDOntologyClassEntry(3pm)✨
• Bio::MAGE::Tools::MGEDOntologyEntry(3pm)✨
• Bio::MAGE::Tools::MGEDOntologyHelper(3pm)✨
• Bio::MAGE::Tools::MGEDOntologyPropertyEntry(3pm)✨
• Bio::MAGE::XML::Handler(3pm)✨
• Bio::MAGE::XML::Handler::ObjectHandler::SQL(3pm)DESCRIPTION of Object✨
• Bio::MAGE::XML::Handler::ObjectHandlerI(3pm)Abstract class for processing Bio::MAGE objects.✨
• Bio::MAGE::XML::Reader(3pm)a module for exporting MAGE-ML✨
• Bio::MAGE::XML::Writer(3pm)a module for exporting MAGE-ML✨
• Bio::Matrix::Generic(3pm)A generic matrix implementation✨
• Bio::Matrix::IO(3pm)A factory for Matrix parsing✨
• Bio::Matrix::IO::mlagan(3pm)A parser for the mlagan substitution matrix✨
• Bio::Matrix::IO::phylip(3pm)A parser for PHYLIP distance matricies✨
• Bio::Matrix::IO::scoring(3pm)A parser for PAM/BLOSUM matricies✨
• Bio::Matrix::MatrixI(3pm)An interface for describing a Matrix✨
• Bio::Matrix::Mlagan(3pm)A generic matrix with mlagan fields✨
• Bio::Matrix::PhylipDist(3pm)A Phylip Distance Matrix object✨
• Bio::Matrix::PSM::InstanceSite(3pm)A PSM site occurrence✨
• Bio::Matrix::PSM::InstanceSiteI(3pm)InstanceSite interface, holds an instance of a PSM✨
• Bio::Matrix::PSM::IO(3pm)PSM parser✨
• Bio::Matrix::PSM::IO::mast(3pm)PSM mast parser implementation✨
• Bio::Matrix::PSM::IO::masta(3pm)motif fasta format parser✨
• Bio::Matrix::PSM::IO::meme(3pm)PSM meme parser implementation✨
• Bio::Matrix::PSM::IO::psiblast(3pm)PSM psiblast parser✨
• Bio::Matrix::PSM::IO::transfac(3pm)PSM transfac parser✨
• Bio::Matrix::PSM::ProtMatrix(3pm)SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.✨
• Bio::Matrix::PSM::ProtPsm(3pm)handle combination of site matricies✨
• Bio::Matrix::PSM::Psm(3pm)handle combination of site matricies✨
• Bio::Matrix::PSM::PsmHeader(3pm)PSM mast parser implementation✨
• Bio::Matrix::PSM::PsmHeaderI(3pm)handles the header data from a PSM file✨
• Bio::Matrix::PSM::PsmI(3pm)abstract interface to handler of site matricies✨
• Bio::Matrix::PSM::SiteMatrix(3pm)SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds✨
• Bio::Matrix::PSM::SiteMatrixI(3pm)SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds✨
• Bio::Matrix::Scoring(3pm)Object which can hold scoring matrix information✨
• Bio::Ontology::DocumentRegistry(3pm)Keep track of where to find ontologies. Allows lookups by name.✨
• Bio::Ontology::GOterm(3pm)representation of GO terms✨
• Bio::Ontology::InterProTerm(3pm)Implementation of InterProI term interface✨
• Bio::Ontology::OBOEngine(3pm)An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium✨
• Bio::Ontology::OBOterm(3pm)representation of OBO terms✨
• Bio::Ontology::Ontology(3pm)standard implementation of an Ontology✨
• Bio::Ontology::OntologyEngineI(3pm)Interface a minimal Ontology implementation should satisfy✨
• Bio::Ontology::OntologyI(3pm)Interface for an ontology implementation✨
• Bio::Ontology::OntologyStore(3pm)A repository of ontologies✨
• Bio::Ontology::Path(3pm)a path for an ontology term graph✨
• Bio::Ontology::PathI(3pm)Interface for a path between ontology terms✨
• Bio::Ontology::Relationship(3pm)a relationship for an ontology✨
• Bio::Ontology::RelationshipFactory(3pm)Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory✨
• Bio::Ontology::RelationshipI(3pm)Interface for a relationship between ontology terms✨
• Bio::Ontology::RelationshipType(3pm)a relationship type for an ontology✨
• Bio::Ontology::SimpleGOEngine::GraphAdaptor(3pm)Graph adaptor for Bio::Ontology::SimpleGOEngine✨
• Bio::Ontology::SimpleOntologyEngine(3pm)Implementation of OntologyEngineI interface✨
• Bio::Ontology::Term(3pm)implementation of the interface for ontology terms✨
• Bio::Ontology::TermFactory(3pm)Instantiates a new Bio::Ontology::TermI (or derived class) through a factory✨
• Bio::Ontology::TermI(3pm)interface for ontology terms✨
• Bio::OntologyIO(3pm)Parser factory for Ontology formats✨
• Bio::OntologyIO::dagflat(3pm)a base class parser for GO flat-file type formats✨
• Bio::OntologyIO::goflat(3pm)a parser for the Gene Ontology flat-file format✨
• Bio::OntologyIO::Handlers::BaseSAXHandler(3pm)base class for SAX Handlers✨
• Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)parse an InterPro XML file and persist the resulting terms to a Biosql database✨
• Bio::OntologyIO::Handlers::InterProHandler(3pm)XML handler class for InterProParser✨
• Bio::OntologyIO::InterProParser(3pm)Parser for InterPro xml files.✨
• Bio::OntologyIO::obo(3pm)parser for OBO flat-file format✨
• Bio::OntologyIO::simplehierarchy(3pm)a base class parser for simple hierarchy-by-indentation type formats✨
• Bio::OntologyIO::soflat(3pm)a parser for the Sequence Ontology flat-file format✨
• Bio::ParameterBaseI(3pm)Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.✨
• Bio::Perl(3pm)Functional access to BioPerl for people who don't know objects✨
• Bio::PrimarySeq(3pm)Bioperl lightweight sequence object✨
• Bio::PrimarySeqI(3pm)Interface definition for a Bio::PrimarySeq✨
• Bio::PrimerDesigner(3pm)Design PCR Primers using primer3 and epcr✨
• Bio::PrimerDesigner::epcr(3pm)A class for accessing the epcr binary✨
• Bio::PrimerDesigner::ispcr(3pm)A class for accessing the isPcr (in-silico PCR) binary✨
• Bio::PrimerDesigner::primer3(3pm)An class for accessing primer3✨
• Bio::PrimerDesigner::Remote(3pm)A class for remote access to Bio::PrimerDesigner✨
• Bio::PrimerDesigner::Result(3pm)a class for handling primer design or validation results✨
• Bio::PrimerDesigner::Tables(3pm)Draw HTML tables for PCR primer display✨
• Bio::Procedural(3pm)Simple low-dependency procedural interfaces to BioPerl✨
• Bio::PullParserI(3pm)A base module for fast 'pull' parsing✨
• Bio::Range(3pm)Pure perl RangeI implementation✨
• Bio::RangeI(3pm)Range interface✨
• Bio::Roary(3pm)Create a pan genome✨
• Bio::Roary::AccessoryBinaryFasta(3pm)Output a FASTA file which represents the binary presence and absence of genes in the accessory genome✨
• Bio::Roary::AccessoryClustering(3pm)Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters✨
• Bio::Roary::AnalyseGroups(3pm)Take in a groups file and the original FASTA files and create plots and stats✨
• Bio::Roary::AnnotateGroups(3pm)Take in a group file and associated GFF files for the isolates and update the group name to the gene name✨
• Bio::Roary::AssemblyStatistics(3pm)Given a spreadsheet of gene presence and absence calculate some statistics✨
• Bio::Roary::BedFromGFFRole(3pm)A role to create a bed file from a gff✨
• Bio::Roary::ChunkFastaFile(3pm)Take in a FASTA file and chunk it up into smaller pieces.✨
• Bio::Roary::ClustersRole(3pm)A role to read a clusters file from CD hit✨
• Bio::Roary::CombinedProteome(3pm)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(3pm)Given a spreadsheet of gene presence and absence calculate some statistics✨
• Bio::Roary::CommandLine::Common(3pm)Common command line settings✨
• Bio::Roary::CommandLine::CreatePanGenome(3pm)Take in FASTA files of proteins and cluster them✨
• Bio::Roary::CommandLine::ExtractProteomeFromGff(3pm)Take in GFF files and output the proteome✨
• Bio::Roary::CommandLine::GeneAlignmentFromNucleotides(3pm)Take in a multifasta file of nucleotides, convert to proteins and align with PRANK✨
• Bio::Roary::CommandLine::IterativeCdhit(3pm)Iteratively run cdhit✨
• Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp(3pm)Take in a FASTA file of proteins and blast against itself✨
• Bio::Roary::CommandLine::QueryRoary(3pm)Take in a groups file and the protein fasta files and output selected data✨
• Bio::Roary::CommandLine::Roary(3pm)Take in FASTA files of proteins and cluster them✨
• Bio::Roary::CommandLine::RoaryCoreAlignment(3pm)Take in the group statistics spreadsheet and the location of the gene multifasta files and create a core alignment.✨
• Bio::Roary::CommandLine::RoaryPostAnalysis(3pm)Perform the post analysis on the pan genome✨
• Bio::Roary::CommandLine::RoaryReorderSpreadsheet(3pm)Take in a tree and a spreadsheet and output a reordered spreadsheet✨
• Bio::Roary::CommandLine::TransferAnnotationToGroups(3pm)Take in a groups file and a set of GFF files and transfer the consensus annotation✨
• Bio::Roary::CommandLine::UniqueGenesPerSample(3pm)Take in the clustered file and produce a sorted file with the frequency of each samples unique genes✨
• Bio::Roary::ContigsToGeneIDsFromGFF(3pm)Parse a GFF and efficiently and extract ordered gene ids on each contig✨
• Bio::Roary::Exceptions(3pm)Exceptions for input data✨
• Bio::Roary::External::Blastp(3pm)Wrapper around NCBIs blastp command✨
• Bio::Roary::External::Cdhit(3pm)Wrapper to run cd-hit✨
• Bio::Roary::External::CheckTools(3pm)Check external executables are available and are the correct version✨
• Bio::Roary::External::Fasttree(3pm)Wrapper to run Fasttree✨
• Bio::Roary::External::GeneAlignmentFromNucleotides(3pm)Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT✨
• Bio::Roary::External::IterativeCdhit(3pm)Iteratively run CDhit✨
• Bio::Roary::External::Mafft(3pm)Wrapper to run mafft✨
• Bio::Roary::External::Makeblastdb(3pm)Wrapper around NCBIs makeblastdb command✨
• Bio::Roary::External::Mcl(3pm)Wrapper around MCL which takes in blast results and outputs clustered results✨
• Bio::Roary::External::PostAnalysis(3pm)Perform the post analysis✨
• Bio::Roary::External::Prank(3pm)Wrapper to run prank✨
• Bio::Roary::ExtractCoreGenesFromSpreadsheet(3pm)Take in a spreadsheet produced by the pipeline and identify the core genes.✨
• Bio::Roary::ExtractProteomeFromGFF(3pm)Take in a GFF file and create protein sequences in FASTA format✨
• Bio::Roary::ExtractProteomeFromGFFs(3pm)Take in GFF files and create protein sequences in FASTA format✨
• Bio::Roary::FilterFullClusters(3pm)Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters✨
• Bio::Roary::FilterUnknownsFromFasta(3pm)Take in fasta files, remove sequences with too many unknowns and return a list of the new files✨
• Bio::Roary::GeneNamesFromGFF(3pm)Parse a GFF and efficiently extract ID -> Gene Name✨
• Bio::Roary::GroupLabels(3pm)Add labels to the groups✨
• Bio::Roary::GroupStatistics(3pm)Add labels to the groups✨
• Bio::Roary::InflateClusters(3pm)Take the clusters file from cd-hit and use it to inflate the output of MCL✨
• Bio::Roary::IterativeCdhit(3pm)Run CDhit iteratively with reducing thresholds, removing full clusters each time✨
• Bio::Roary::JobRunner::Local(3pm)Execute a set of commands locally✨
• Bio::Roary::JobRunner::Parallel(3pm)Use GNU Parallel✨
• Bio::Roary::JobRunner::Role(3pm)A role to add job runner functionality✨
• Bio::Roary::LookupGeneFiles(3pm)Take in an ordering of genes and a directory and return an ordered list of file locations✨
• Bio::Roary::MergeMultifastaAlignments(3pm)Merge multifasta alignment files with equal numbers of sequences.✨
• Bio::Roary::OrderGenes(3pm)Take in GFF files and create a matrix of what genes are beside what other genes✨
• Bio::Roary::Output::BlastIdentityFrequency(3pm)Take in blast results and find the percentage identity graph✨
• Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL(3pm)Create an embl file for the header with locations of where genes are in the multifasta alignment of core genes✨
• Bio::Roary::Output::DifferenceBetweenSets(3pm)Given two sets of isolates and a group file, output whats unique in each and whats in common✨
• Bio::Roary::Output::EmblGroups(3pm)Create a tab/embl file with the features for drawing pretty pictures✨
• Bio::Roary::Output::EMBLHeaderCommon(3pm)a role containing some common methods for embl header files✨
• Bio::Roary::Output::GroupMultifasta(3pm)Take in a group and create a multifasta file✨
• Bio::Roary::Output::GroupsMultifastaNucleotide(3pm)Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences.✨
• Bio::Roary::Output::GroupsMultifastaProtein(3pm)Take a multifasta nucleotide file and output it as proteins.✨
• Bio::Roary::Output::GroupsMultifastas(3pm)Take in a list of groups and create multifastas files for each group✨
• Bio::Roary::Output::GroupsMultifastasNucleotide(3pm)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(3pm)Create raw output files of group counts for turning into plots✨
• Bio::Roary::Output::QueryGroups(3pm)Output the groups of the union of a set of input isolates✨
• Bio::Roary::ParallelAllAgainstAllBlast(3pm)Run all against all blast in parallel✨
• Bio::Roary::ParseGFFAnnotationRole(3pm)A role for parsing a gff file efficiently✨
• Bio::Roary::PostAnalysis(3pm)Post analysis of pan genomes✨
• Bio::Roary::PrepareInputFiles(3pm)Take in a mixture of FASTA and GFF input files and output FASTA proteomes only✨
• Bio::Roary::PresenceAbsenceMatrix(3pm)Create a matrix with presence and absence✨
• Bio::Roary::QC::Report(3pm)generate a report based on kraken output✨
• Bio::Roary::ReformatInputGFFs(3pm)Take in gff files and add suffix where a gene id is seen twice✨
• Bio::Roary::ReorderSpreadsheet(3pm)Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns✨
• Bio::Roary::SampleOrder(3pm)Take in a tree file and return an ordering of the samples✨
• Bio::Roary::SequenceLengths(3pm)Take in a fasta file and create a hash with the length of each sequence✨
• Bio::Roary::SortFasta(3pm)sort a fasta file by name✨
• Bio::Roary::SplitGroups(3pm)split groups✨
• Bio::Roary::SpreadsheetRole(3pm)Read and write a spreadsheet✨
• Bio::Roary::UniqueGenesPerSample(3pm)Take in the clustered file and produce a sorted file with the frequency of each samples unique genes✨
• Bio::Root::Exception(3pm)BioPerl exceptions✨
• Bio::Root::HTTPget(3pm)module for fallback HTTP get operations when LWP:: is unavailable✨
• Bio::Root::IO(3pm)BioPerl base IO handling class✨
• Bio::Root::Root(3pm)implementation of Bio::Root::RootI interface✨
• Bio::Root::RootI(3pm)base interface for all BioPerl classes✨
• Bio::Root::Storable(3pm)Safely store/retrieve objects from disk✨
• Bio::Root::Test(3pm)common base for all BioPerl test scripts✨
• Bio::Root::TestObject(3pm)An implementation of TestInterface✨
• Bio::Root::Utilities(3pm)general-purpose utilities✨
• Bio::Root::Version(3pm)don't use, get version from each module✨
• Bio::SCF(3pm)Perl extension for reading and writing SCF sequence files✨
• Bio::Search::BlastStatistics(3pm)An object for Blast statistics✨
• Bio::Search::BlastUtils(3pm)Utility functions for Bio::Search:: BLAST objects✨
• Bio::Search::DatabaseI(3pm)Interface for a database used in a sequence search✨
• Bio::Search::GenericDatabase(3pm)Generic implementation of Bio::Search::DatabaseI✨
• Bio::Search::GenericStatistics(3pm)An object for statistics✨
• Bio::Search::Hit::BlastHit(3pm)Blast-specific subclass of Bio::Search::Hit::GenericHit✨
• Bio::Search::Hit::BlastPullHit(3pm)A parser and hit object for BLASTN hits✨
• Bio::Search::Hit::Fasta(3pm)Hit object specific for Fasta-generated hits✨
• Bio::Search::Hit::GenericHit(3pm)A generic implementation of the Bio::Search::Hit::HitI interface✨