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::DB::Fasta
- Fast indexed access to fasta files
- Bio::DB::FileCache
- In file cache for BioSeq objects
- Bio::DB::Flat
- Interface for indexed flat files
- Bio::DB::Flat::BDB
- Interface for BioHackathon standard BDB-indexed flat file
- Bio::DB::Flat::BDB::embl
- embl adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BDB::fasta
- fasta adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BDB::genbank
- genbank adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BDB::swiss
- swissprot adaptor for Open-bio standard BDB-indexed flat file
- Bio::DB::Flat::BinarySearch
- BinarySearch search indexing system for sequence files
- Bio::DB::GFF::Aggregator::match_gap
- - GFF3 match aggregator
- Bio::DB::GFF::Aggregator::reftranscript
- - Aggregates references transcripts
- Bio::DB::GFF::Aggregator::waba_alignment
- - A WABA alignment
- Bio::DB::GFF::Aggregator::wormbase_gene
- - Wormbase gene aggregator
- Bio::DB::GFF::Util::Binning
- binning utility for Bio::DB::GFF index
- Bio::DB::GFF::Util::Rearrange
- rearrange utility
- Bio::DB::GenericWebAgent
- helper base class for parameter-based remote server access and response retrieval
- Bio::DB::HTS
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::AlignWrapper
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Alignment
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Constants
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Faidx
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::FetchIterator
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Kseq
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Kseq::Iterator
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Kseq::Record
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Pileup
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::PileupWrapper
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Query
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::ReadIterator
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Segment
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Tabix
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Tabix::Iterator
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::Target
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::VCF
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::HTS::VCF::Iterator
- Copyright [2015-2018] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
- Bio::DB::InMemoryCache
- Abstract interface for a sequence database
- Bio::DB::IndexedBase
- Base class for modules using indexed sequence files
- Bio::DB::LocationI
- A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
- Bio::DB::Qual
- Fast indexed access to quality files
- Bio::DB::Query::WebQuery
- Helper class for web-based sequence queryies
- Bio::DB::QueryI
- Object Interface to queryable sequence databases
- Bio::DB::RandomAccessI
- Abstract interface for a sequence database
- Bio::DB::ReferenceI
- A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
- Bio::DB::Registry
- Access to the Open Bio Database Access registry scheme
- Bio::DB::Sam
- - Read SAM/BAM database files
- Bio::DB::Sam::Constants
- - Constants for use with SAM/BAM
- Bio::DB::SeqFeature::Store::Alias
- - override feature type, method, source and attribute fields
- Bio::DB::SeqI
- Abstract Interface for Sequence databases
- Bio::DB::SoapEUtilities
- Interface to the NCBI Entrez web service *BETA*
- Bio::DB::SoapEUtilities::DocSumAdaptor
- Handle for Entrez SOAP DocSums
- Bio::DB::SoapEUtilities::FetchAdaptor
- Conversion of Entrez SOAP messages to BioPerl objects
- Bio::DB::SoapEUtilities::FetchAdaptor::seq
- Fetch adaptor for 'seq' efetch SOAP messages
- Bio::DB::SoapEUtilities::FetchAdaptor::species
- Fetch adaptor for 'taxonomy' efetch SOAP messages
- Bio::DB::SoapEUtilities::GQueryAdaptor
- Handle for Entrez SOAP GlobalQuery items
- Bio::DB::SoapEUtilities::LinkAdaptor
- Handle for Entrez SOAP LinkSets
- Bio::DB::SoapEUtilities::Result
- Accessor object for SoapEUtilities results
- Bio::DB::Tagger
- - Simple object tagging system
- Bio::DB::Tagger::Tag
- - Authored tags
- Bio::DB::Taxonomy
- Access to a taxonomy database
- Bio::DB::Taxonomy::flatfile
- Use the NCBI taxonomy from local indexed flat files
- Bio::DB::Taxonomy::greengenes
- Use the Greengenes taxonomy
- Bio::DB::Taxonomy::list
- An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
- Bio::DB::Taxonomy::silva
- Use the Silva taxonomy
- Bio::DB::UpdateableSeqI
- An interface for writing to a database of sequences
- Bio::DB::WebDBSeqI
- Object Interface to generalize Web Databases for retrieving sequences
- Bio::DBLinkContainerI
- Abstract interface for any object wanting to use database cross references
- Bio::Das::FeatureTypeI
- Simple interface to Sequence Ontology feature types
- Bio::Das::SegmentI
- DAS-style access to a feature database
- Bio::DasI
- DAS-style access to a feature database
- Bio::DescribableI
- interface for objects with human readable names and descriptions
- Bio::Event::EventGeneratorI
- This interface describes the basic event generator class
- Bio::Event::EventHandlerI
- An Event Handler Interface
- Bio::Factory::AnalysisI
- An interface to analysis tool factory
- Bio::Factory::ApplicationFactoryI
- Interface class for Application Factories
- Bio::Factory::DriverFactory
- Base class for factory classes loading drivers
- Bio::Factory::EMBOSS
- EMBOSS application factory class
- Bio::Factory::FTLocationFactory
- A FeatureTable Location Parser
- Bio::Factory::LocationFactoryI
- A factory interface for generating locations from a string
- Bio::Factory::ObjectBuilderI
- Interface for an object builder
- Bio::Factory::ObjectFactory
- Instantiates a new Bio::Root::RootI (or derived class) through a factory
- Bio::Factory::ObjectFactoryI
- A General object creator factory
- Bio::Factory::SeqAnalysisParserFactory
- class capable of creating SeqAnalysisParserI compliant parsers
- Bio::Factory::SeqAnalysisParserFactoryI
- interface describing objects capable of creating SeqAnalysisParserI compliant parsers
- Bio::Factory::SequenceFactoryI
- This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
- Bio::Factory::SequenceProcessorI
- Interface for chained sequence processing algorithms
- Bio::Factory::SequenceStreamI
- Interface describing the basics of a Sequence Stream
- Bio::Factory::TreeFactoryI
- Factory Interface for getting and writing trees from/to a data stream
- Bio::FeatureHolderI
- the base interface an object with features must implement
- Bio::Graphics::Browser2::AuthorizedFeatureFile
- - Add HTTP authorization features to FeatureFile
- Bio::Graphics::Browser2::CAlign
- Compiled helper for Bio::Graphics::Browser::Realign
- Bio::Graphics::Browser2::DataBase
- - A simple cache for database handles
- Bio::Graphics::Browser2::DataLoader::archive
- data loader for archives of BigWig files
- Bio::Graphics::Browser2::DataLoader::useq
- data loader for the USeq archive
- Bio::Graphics::Browser2::DataSource
- - DataSource to access data
- Bio::Graphics::Browser2::GFFhelper
- - Helps gbrowse plugins handle GFF
- Bio::Graphics::Browser2::Markup
- Markup routines for sequences in text form
- Bio::Graphics::Browser2::OptionPick
- - Pick options
- Bio::Graphics::Browser2::PadAlignment
- Insert pads into a multiple alignment
- Bio::Graphics::Browser2::Plugin
- - Base class for gbrowse plugins
- Bio::Graphics::Browser2::Plugin::AuthPlugin
- - Base class for authentication plugins