### Home Classes Methods

### In Files

- lib/bio/db/kegg/genes.rb

### Parent

KEGGDB

### Methods

- ::new
- #aalen
- #aaseq
- #chromosome
- #codon_usage
- #cu_list
- #dblinks
- #dblinks_as_hash
- #dblinks_as_strings
- #definition
- #division
- #eclinks
- #entry
- #entry_id
- #gbposition
- #gene
- #genes
- #keggclass
- #keggclasses
- #locations
- #motif
- #motifs
- #motifs_as_hash
- #motifs_as_strings
- #nalen
- #name
- #names
- #names_as_array
- #naseq
- #ntlen
- #ntseq
- #organism
- #orthologs
- #orthologs_as_hash
- #orthologs_as_strings
- #pathway
- #pathways
- #pathways_as_hash
- #pathways_as_strings
- #position
- #structure
- #structures

### Included Modules

- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::OrthologsAsHash

### Files

- KNOWN_ISSUES.rdoc
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
- Bio::Alignment
- Bio::Alignment::ArrayExtension
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- Bio::Blast::Bl2seq::Report::Iteration
- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
- Bio::Blast::Default::Report::Hit
- Bio::Blast::Default::Report::Iteration
- Bio::Blast::Default::Report_TBlast
- Bio::Blast::Fastacmd
- Bio::Blast::NCBIOptions
- Bio::Blast::RPSBlast
- Bio::Blast::RPSBlast::RPSBlastSplitter
- Bio::Blast::RPSBlast::Report
- Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER
- Bio::Blast::RPSBlast::Report::Iteration
- Bio::Blast::Remote
- Bio::Blast::Remote::DDBJ
- Bio::Blast::Remote::DDBJ::Information
- Bio::Blast::Remote::Ddbj
- Bio::Blast::Remote::GenomeNet
- Bio::Blast::Remote::GenomeNet::Information
- Bio::Blast::Remote::Genomenet
- Bio::Blast::Remote::Information
- Bio::Blast::Report
- Bio::Blast::Report::BlastXmlSplitter
- Bio::Blast::Report::FLATFILE_SPLITTER
- Bio::Blast::Report::Hit
- Bio::Blast::Report::Hsp
- Bio::Blast::Report::Iteration
- Bio::Blast::Report_tab
- Bio::Blast::WU
- Bio::Blast::WU::Report
- Bio::Blast::WU::Report::HSP
- Bio::Blast::WU::Report::Hit
- Bio::Blast::WU::Report::Iteration
- Bio::Blast::WU::Report_TBlast
- Bio::Blat
- Bio::Blat::Report
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
- Bio::DAS::TARGET
- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DBGET
- Bio::DDBJ
- Bio::DDBJ::REST
- Bio::DDBJ::REST::Blast
- Bio::DDBJ::REST::ClustalW
- Bio::DDBJ::REST::DDBJ
- Bio::DDBJ::REST::Mafft
- Bio::DDBJ::REST::RequestManager
- Bio::DDBJ::REST::WABItemplate
- Bio::DDBJ::XML
- Bio::DDBJ::XML::Blast
- Bio::DDBJ::XML::ClustalW
- Bio::DDBJ::XML::DDBJ
- Bio::DDBJ::XML::Fasta
- Bio::DDBJ::XML::GetEntry
- Bio::DDBJ::XML::Gib
- Bio::DDBJ::XML::Gtop
- Bio::DDBJ::XML::PML
- Bio::DDBJ::XML::RequestManager
- Bio::DDBJ::XML::RequestManager::REST
- Bio::DDBJ::XML::SRS
- Bio::DDBJ::XML::TxSearch
- Bio::EBI
- Bio::EBI::SOAP
- Bio::EBI::SOAP::Citation
- Bio::EBI::SOAP::ClustalW
- Bio::EBI::SOAP::Dbfetch
- Bio::EBI::SOAP::Emboss
- Bio::EBI::SOAP::Fasta
- Bio::EBI::SOAP::InterProScan
- Bio::EBI::SOAP::MPsrch
- Bio::EBI::SOAP::MSD
- Bio::EBI::SOAP::Muscle
- Bio::EBI::SOAP::Ontology
- Bio::EBI::SOAP::ScanPS
- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::References
- Bio::KEGG::Common::StringsAsHash
- Bio::KEGG::DRUG
- Bio::KEGG::ENZYME
- Bio::KEGG::EXPRESSION
- Bio::KEGG::GENES
- Bio::KEGG::GENOME
- Bio::KEGG::GLYCAN
- Bio::KEGG::KGML
- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
- Bio::KEGG::KGML::Product
- Bio::KEGG::KGML::Reaction
- Bio::KEGG::KGML::Relation
- Bio::KEGG::KGML::Substrate
- Bio::KEGG::KGML::SubstrateProduct
- Bio::KEGG::Keggtab
- Bio::KEGG::Keggtab::DB
- Bio::KEGG::MODULE
- Bio::KEGG::ORTHOLOGY
- Bio::KEGG::PATHWAY
- Bio::KEGG::REACTION
- Bio::KEGG::Taxonomy
- Bio::KEGGDB
- Bio::LITDB
- Bio::Lasergene
- Bio::Location
- Bio::Locations
- Bio::MAFFT
- Bio::MAFFT::Report
- Bio::MEDLINE
- Bio::Map
- Bio::Map::ActsLikeMap
- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
- Bio::Map::Marker
- Bio::Map::SimpleMap
- Bio::Meme
- Bio::Meme::Mast
- Bio::Meme::Mast::Report
- Bio::Meme::Motif
- Bio::Muscle
- Bio::Muscle::DEFAULT_PARSER
- Bio::NBRF
- Bio::NCBI
- Bio::NCBI::REST
- Bio::NCBI::REST::EFetch
- Bio::NCBI::REST::EFetch::Methods
- Bio::NCBI::REST::ESearch
- Bio::NCBI::REST::ESearch::Methods
- Bio::NCBI::SOAP
- Bio::NCBI::SOAP::EFetch
- Bio::NCBI::SOAP::EFetchLite
- Bio::NCBI::SOAP::EUtils
- Bio::NCBI::SOAP::EUtilsLite
- Bio::NCBIDB
- Bio::NCBIDB::Common
- Bio::Newick
- Bio::Newick::ParseError
- Bio::Nexus
- Bio::Nexus::CharactersBlock
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
- Bio::Nexus::TaxaBlock
- Bio::Nexus::TreesBlock
- Bio::Nexus::Util
- Bio::NucleicAcid
- Bio::NucleicAcid::Data
- Bio::PAML
- Bio::PAML::Baseml
- Bio::PAML::Baseml::Report
- Bio::PAML::Codeml
- Bio::PAML::Codeml::Model
- Bio::PAML::Codeml::PositiveSite
- Bio::PAML::Codeml::PositiveSites
- Bio::PAML::Codeml::Rates
- Bio::PAML::Codeml::Report
- Bio::PAML::Codeml::ReportError
- Bio::PAML::Codeml::ReportSingle
- Bio::PAML::Common
- Bio::PAML::Common::Report
- Bio::PAML::Yn00
- Bio::PAML::Yn00::Report
- Bio::PDB
- Bio::PDB::AtomFinder
- Bio::PDB::Chain
- Bio::PDB::ChainFinder
- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
- Bio::PDB::DataType
- Bio::PDB::DataType::ConstLikeMethod
- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
- Bio::PDB::DataType::Pdb_Character
- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
- Bio::PDB::DataType::Pdb_Integer
- Bio::PDB::DataType::Pdb_LString
- Bio::PDB::DataType::Pdb_List
- Bio::PDB::DataType::Pdb_Real
- Bio::PDB::DataType::Pdb_Residue_name
- Bio::PDB::DataType::Pdb_SList
- Bio::PDB::DataType::Pdb_Specification_list
- Bio::PDB::DataType::Pdb_String
- Bio::PDB::DataType::Pdb_StringRJ
- Bio::PDB::DataType::Pdb_SymOP
- Bio::PDB::HetatmFinder
- Bio::PDB::Heterogen
- Bio::PDB::HeterogenFinder
- Bio::PDB::Model
- Bio::PDB::ModelFinder
- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
- Bio::PDB::Record::ATOM
- Bio::PDB::Record::HETATM
- Bio::PDB::Record::Jrnl
- Bio::PDB::Record::Remark1
- Bio::PDB::Record::Remark2
- Bio::PDB::Residue
- Bio::PDB::ResidueFinder
- Bio::PDB::Utils
- Bio::PROSITE
- Bio::PSORT
- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
- Bio::PSORT::PSORT1::Report
- Bio::PSORT::PSORT2
- Bio::PSORT::PSORT2::Remote
- Bio::PSORT::PSORT2::Report
- Bio::PSORT::PSORTB
- Bio::PSORT::WoLF_PSORT
- Bio::PTS1
- Bio::PTS1::Report
- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::PhyloXML
- Bio::PhyloXML::Accession
- Bio::PhyloXML::Annotation
- Bio::PhyloXML::BinaryCharacters
- Bio::PhyloXML::BranchColor
- Bio::PhyloXML::CladeRelation
- Bio::PhyloXML::Confidence
- Bio::PhyloXML::Date
- Bio::PhyloXML::Distribution
- Bio::PhyloXML::DomainArchitecture
- Bio::PhyloXML::Events
- Bio::PhyloXML::Id
- Bio::PhyloXML::Node
- Bio::PhyloXML::Other
- Bio::PhyloXML::Parser
- Bio::PhyloXML::Point
- Bio::PhyloXML::Polygon
- Bio::PhyloXML::Property
- Bio::PhyloXML::ProteinDomain
- Bio::PhyloXML::Reference
- Bio::PhyloXML::Sequence
- Bio::PhyloXML::SequenceRelation
- Bio::PhyloXML::Taxonomy
- Bio::PhyloXML::Tree
- Bio::PhyloXML::Uri
- Bio::PhyloXML::Writer
- Bio::Probcons
- Bio::PubMed
- Bio::REBASE
- Bio::RefSeq
- Bio::Reference
- Bio::References
- Bio::Registry
- Bio::Registry::DB
- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
- Bio::SOFT
- Bio::SOSUI
- Bio::SOSUI::Report
- Bio::SOSUI::Report::TMH
- Bio::SPTR
- Bio::SQL
- Bio::SQL::Biodatabase
- Bio::SQL::Bioentry
- Bio::SQL::BioentryDbxref
- Bio::SQL::BioentryPath
- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
- Bio::SQL::BioentryRelationship
- Bio::SQL::Biosequence
- Bio::SQL::Comment
- Bio::SQL::Dbxref
- Bio::SQL::DbxrefQualifierValue
- Bio::SQL::DummyBase
- Bio::SQL::Location
- Bio::SQL::LocationQualifierValue
- Bio::SQL::Ontology
- Bio::SQL::Reference
- Bio::SQL::Seqfeature
- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
- Bio::SQL::SeqfeatureRelationship
- Bio::SQL::Sequence
- Bio::SQL::Taxon
- Bio::SQL::TaxonName
- Bio::SQL::Term
- Bio::SQL::TermDbxref
- Bio::SQL::TermPath
- Bio::SQL::TermRelationship
- Bio::SQL::TermRelationshipTerm
- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
- Bio::Sequence::Format::NucFormatter::Embl
- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
- Bio::Sequence::NA::MidiTrack
- Bio::Sequence::QualityScore
- Bio::Sequence::QualityScore::Converter
- Bio::Sequence::QualityScore::Phred
- Bio::Sequence::QualityScore::Solexa
- Bio::Sequence::SequenceMasker
- Bio::Shell
- Bio::Shell::ColoredCodonTable
- Bio::Shell::Core
- Bio::Shell::Demo
- Bio::Shell::Ghost
- Bio::Shell::Irb
- Bio::Shell::Private
- Bio::Shell::Script
- Bio::Shell::Setup
- Bio::Shell::Web
- Bio::Shell::Web::Results
- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
- Bio::Sim4::Report
- Bio::Sim4::Report::Hit
- Bio::Sim4::Report::Segment
- Bio::Sim4::Report::SegmentPair
- Bio::Sim4::Report::SeqDesc
- Bio::Spidey
- Bio::Spidey::Report
- Bio::Spidey::Report::Hit
- Bio::Spidey::Report::Segment
- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
- Bio::TMHMM::Report
- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
- Bio::TRANSFAC::FACTOR
- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
- Bio::TRANSFAC::SITE
- Bio::TargetP
- Bio::TargetP::Report
- Bio::Taxonomy
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
- Bio::Tree::Edge
- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio::KEGG::GENES

## Description

KEGG GENES entry parser.

## References

- www.genome.jp/kegg/genes.html

### Constants

DELIMITER
TAGSIZE

### Public Class Methods

new(entry) click to toggle source

Creates a new Bio::KEGG::GENES object.

Arguments:

- (required) entry: (String) single entry as a string

Returns | Bio::KEGG::GENES object

    # File lib/bio/db/kegg/genes.rb, line 115
    def initialize(entry)
      super(entry, TAGSIZE)
    end

### Public Instance Methods

aalen() click to toggle source

Returns length of the amino acid sequence described in the AASEQ lines.

Returns | Integer

    # File lib/bio/db/kegg/genes.rb, line 393
    def aalen
      fetch('AASEQ')[/\d+/].to_i
    end

aaseq() click to toggle source

Returns amino acid sequence described in the AASEQ lines.

Returns | Bio::Sequence::AA object

    # File lib/bio/db/kegg/genes.rb, line 383
    def aaseq
      unless @data['AASEQ']
        @data['AASEQ'] = Bio::Sequence::AA.new(fetch('AASEQ').gsub(/\d+/, ''))
      end
      @data['AASEQ']
    end

chromosome() click to toggle source

Chromosome described in the POSITION line.

Returns | String or nil

    # File lib/bio/db/kegg/genes.rb, line 264
    def chromosome
      if position[/:/]
        position.sub(/:.*/, '')
      elsif ! position[/\.\./]
        position
      else
        nil
      end
    end

codon_usage(codon = nil) click to toggle source

Codon usage data described in the CODON_USAGE lines. (Deprecated: no more exists)

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 350
    def codon_usage(codon = nil)
      unless @data['CODON_USAGE']
        hash = Hash.new
        list = cu_list
        base = %(t c a g)
        base.each_with_index do |x, i|
          base.each_with_index do |y, j|
            base.each_with_index do |z, k|
              hash["#{x}#{y}#{z}"] = list[i*16 + j*4 + k]
            end
          end
        end
        @data['CODON_USAGE'] = hash
      end
      @data['CODON_USAGE']
    end

cu_list() click to toggle source

Codon usage data described in the CODON_USAGE lines as an array.

Returns | Array

    # File lib/bio/db/kegg/genes.rb, line 370
    def cu_list
      ary = []
      get('CODON_USAGE').sub(/.*/,'').each_line do |line| # cut 1st line
        line.chomp.sub(/^.{11}/, '').scan(/..../) do |cu|
          ary.push(cu.to_i)
        end
      end
      return ary
    end

dblinks() click to toggle source
Alias for: dblinks_as_hash
dblinks_as_hash() click to toggle source

Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.

    # File lib/bio/db/kegg/genes.rb, line 97
    def dblinks_as_hash; super; end

Also aliased as: dblinks
dblinks_as_strings() click to toggle source

Links to other databases described in the DBLINKS lines.

Returns | Array containing String objects

    # File lib/bio/db/kegg/genes.rb, line 332
    def dblinks_as_strings
      lines_fetch('DBLINKS')
    end

definition() click to toggle source

Definition of the entry, described in the DEFINITION line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 199
    def definition
      field_fetch('DEFINITION')
    end

division() click to toggle source

Division of the entry, described in the ENTRY line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 149
    def division
      entry['division']                   # CDS, tRNA etc.
    end

eclinks() click to toggle source

Enzyme's EC numbers shown in the DEFINITION line.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 206
    def eclinks
      unless defined? @eclinks
        ec_list =
          definition.slice(/\[EC\:([^\]]+)\]/, 1) ||
          definition.slice(/\(EC\:([^\)]+)\)/, 1)
        ary = ec_list ? ec_list.strip.split(/\s+/) : []
        @eclinks = ary
      end
      @eclinks
    end

entry() click to toggle source

Returns the "ENTRY" line content as a Hash. For example,

    {"organism"=>"E.coli", "division"=>"CDS", "id"=>"b0356"}

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 125
    def entry
      unless @data['ENTRY']
        hash = Hash.new('')
        if get('ENTRY').length > 30
          e = get('ENTRY')
          hash['id']       = e[12..29].strip
          hash['division'] = e[30..39].strip
          hash['organism'] = e[40..80].strip
        end
        @data['ENTRY'] = hash
      end
      @data['ENTRY']
    end

entry_id() click to toggle source

ID of the entry, described in the ENTRY line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 142
    def entry_id
      entry['id']
    end

gbposition() click to toggle source

The position in the genome described in the POSITION line as GenBank feature table location formatted string.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 278
    def gbposition
      position.sub(/.*?:/, '')
    end

gene() click to toggle source

The method will be deprecated. Use `entry.names.first` instead.

Returns the first gene name described in the NAME line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 192
    def gene
      genes.first
    end

genes() click to toggle source

The method will be deprecated. Use Bio::KEGG::GENES#names.

Names of the entry as an Array, described in the NAME line.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 182
    def genes
      names_as_array
    end

keggclass() click to toggle source

Returns CLASS field of the entry.

    # File lib/bio/db/kegg/genes.rb, line 242
    def keggclass
      field_fetch('CLASS')
    end

keggclasses() click to toggle source

Returns an Array of biological classes in CLASS field.

    # File lib/bio/db/kegg/genes.rb, line 247
    def keggclasses
      keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
    end

locations() click to toggle source

The position in the genome described in the POSITION line as Bio::Locations object.

Returns | Bio::Locations object

    # File lib/bio/db/kegg/genes.rb, line 286
    def locations
      Bio::Locations.new(gbposition)
    end

motif() click to toggle source

The specification of the method will be changed in the future. Please use Bio::KEGG::GENES#motifs.

Motif information described in the MOTIF lines.

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 325
    def motif
      motifs
    end

motifs() click to toggle source
Alias for: motifs_as_hash
motifs_as_hash() click to toggle source

Motif information described in the MOTIF lines.

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 300
    def motifs_as_hash
      unless @data['MOTIF']
        hash = {}
        db = nil
        motifs_as_strings.each do |line|
          if line[/^\S+:/]
            db, str = line.split(/:/, 2)
          else
            str = line
          end
          hash[db] ||= []
          hash[db] += str.strip.split(/\s+/)
        end
        @data['MOTIF'] = hash
      end
      @data['MOTIF']              # Hash of Array of IDs in MOTIF
    end

Also aliased as: motifs
motifs_as_strings() click to toggle source

Motif information described in the MOTIF lines.

Returns | Strings

    # File lib/bio/db/kegg/genes.rb, line 293
    def motifs_as_strings
      lines_fetch('MOTIF')
    end

nalen() click to toggle source
Alias for: ntlen
name() click to toggle source

Returns the NAME line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 163
    def name
      field_fetch('NAME')
    end

names() click to toggle source
Alias for: names_as_array
names_as_array() click to toggle source

Names of the entry as an Array, described in the NAME line.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 171
    def names_as_array
      name.split(', ')
    end

Also aliased as: names
naseq() click to toggle source
Alias for: ntseq
ntlen() click to toggle source

Returns nucleic acid sequence length.

Returns | Integer

    # File lib/bio/db/kegg/genes.rb, line 411
    def ntlen
      fetch('NTSEQ')[/\d+/].to_i
    end

Also aliased as: nalen
ntseq() click to toggle source

Returns nucleic acid sequence described in the NTSEQ lines.

Returns | Bio::Sequence::NA object

    # File lib/bio/db/kegg/genes.rb, line 400
    def ntseq
      unless @data['NTSEQ']
        @data['NTSEQ'] = Bio::Sequence::NA.new(fetch('NTSEQ').gsub(/\d+/, ''))
      end
      @data['NTSEQ']
    end

Also aliased as: naseq
organism() click to toggle source

Organism name of the entry, described in the ENTRY line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 156
    def organism
      entry['organism']                   # H.sapiens etc.
    end

orthologs() click to toggle source
Alias for: orthologs_as_hash
orthologs_as_hash() click to toggle source

Returns a Hash of the orthology ID and definition in ORTHOLOGY field.

    # File lib/bio/db/kegg/genes.rb, line 107
    def orthologs_as_hash; super; end

Also aliased as: orthologs
orthologs_as_strings() click to toggle source

Orthologs described in the ORTHOLOGY lines.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 220
    def orthologs_as_strings
      lines_fetch('ORTHOLOGY')
    end

pathway() click to toggle source

Returns the PATHWAY lines as a String.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 227
    def pathway
      unless defined? @pathway
        @pathway = fetch('PATHWAY')
      end
      @pathway
    end

pathways() click to toggle source
Alias for: pathways_as_hash
pathways_as_hash() click to toggle source

Returns a Hash of the pathway ID and name in PATHWAY field.

    # File lib/bio/db/kegg/genes.rb, line 102
    def pathways_as_hash; super; end

Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathways described in the PATHWAY lines.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 237
    def pathways_as_strings
      lines_fetch('PATHWAY')
    end

position() click to toggle source

The position in the genome described in the POSITION line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 254
    def position
      unless @data['POSITION']
        @data['POSITION'] = fetch('POSITION').gsub(/\s/, '')
      end
      @data['POSITION']
    end

structure() click to toggle source

Returns structure ID information described in the STRUCTURE lines.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 339
    def structure
      unless @data['STRUCTURE']
        @data['STRUCTURE'] = fetch('STRUCTURE').sub(/(PDB: )*/,'').split(/\s+/)
      end
      @data['STRUCTURE'] # ['PDB:1A9X', ...]
    end

Also aliased as: structures
structures() click to toggle source
Alias for: structure

[Validate]

Generated with the Darkfish Rdoc Generator 2.