### Home Classes Methods

### In Files

- lib/bio/db/embl/embl.rb

### Parent

Bio::EMBLDB

### Methods

- #cc
- #comment
- #data_class
- #date_created
- #date_modified
- #dblinks
- #division
- #dt
- #each_cds
- #each_gene
- #entry
- #entry_id
- #entry_name
- #entry_version
- #features
- #fh
- #ft
- #id_line
- #molecule
- #molecule_type
- #naseq
- #ntseq
- #os
- #release_created
- #release_modified
- #seq
- #seqlen
- #sequence_length
- #species
- #sq
- #sv
- #to_biosequence
- #topology
- #version

### Included Modules

- Bio::EMBLDB::Common

### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- 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
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- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
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- 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
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- Bio::Blast::Remote::DDBJ
- Bio::Blast::Remote::DDBJ::Information
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- Bio::Blast::Report::BlastXmlSplitter
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- Bio::Blast::Report::Hit
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- 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::FLATFILE_SPLITTER
- 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::EMBL

### Public Instance Methods

cc() click to toggle source

returns comment text in the comments (CC) line.

CC Line; comments of notes (>=0)

    # File lib/bio/db/embl/embl.rb, line 401
    def cc
      get('CC').to_s.gsub(/^CC   /, '')
    end

Also aliased as: comment
comment() click to toggle source
Alias for: cc
data_class() click to toggle source

    # File lib/bio/db/embl/embl.rb, line 130
    def data_class
      id_line('DATA_CLASS')
    end

date_created() click to toggle source

created date. Returns Date object, String or nil.

    # File lib/bio/db/embl/embl.rb, line 461
    def date_created
      parse_date(self.dt['created'])
    end

date_modified() click to toggle source

modified date. Returns Date object, String or nil.

    # File lib/bio/db/embl/embl.rb, line 456
    def date_modified
      parse_date(self.dt['updated'])
    end

dblinks() click to toggle source

database references (DR). Returns an array of Bio::Sequence::DBLink objects.

    # File lib/bio/db/embl/embl.rb, line 511
    def dblinks
      get('DR').split(/\n/).collect { |x|
        Bio::Sequence::DBLink.parse_embl_DR_line(x)
      }
    end

division() click to toggle source

returns DIVISION in the ID line.

- Bio::EMBL#division -> String

    # File lib/bio/db/embl/embl.rb, line 140
    def division
      id_line('DIVISION')
    end

dt(key=nil) click to toggle source

returns contents in the date (DT) line.

- Bio::EMBL#dt -> <DT Hash>

where <DT Hash> is:

    {}

- Bio::EMBL#dt(key) -> String

keys: 'created' and 'updated'

DT Line; date (2/entry)

    # File lib/bio/db/embl/embl.rb, line 182
    def dt(key=nil)
      unless @data['DT']
        tmp = Hash.new
        dt_line = self.get('DT').split(/\n/)
        tmp['created'] = dt_line[0].sub(/\w{2}   /,'').strip
        tmp['updated'] = dt_line[1].sub(/\w{2}   /,'').strip
        @data['DT'] = tmp
      end
      if key
        @data['DT'][key]
      else
        @data['DT']
      end
    end

each_cds() click to toggle source

iterates on CDS features in the FT lines.

    # File lib/bio/db/embl/embl.rb, line 380
    def each_cds
      ft.each do |cds_feature|
        if cds_feature.feature == 'CDS'
          yield cds_feature
        end
      end
    end

each_gene() click to toggle source

iterates on gene features in the FT lines.

    # File lib/bio/db/embl/embl.rb, line 389
    def each_gene
      ft.each do |gene_feature|
        if gene_feature.feature == 'gene'
          yield gene_feature
        end
      end
    end

entry() click to toggle source

returns ENTRY_NAME in the ID line.

- Bio::EMBL#entry -> String

    # File lib/bio/db/embl/embl.rb, line 117
    def entry
      id_line('ENTRY_NAME')
    end

Also aliased as: entry_name, entry_id
entry_id() click to toggle source
Alias for: entry
entry_name() click to toggle source
Alias for: entry
entry_version() click to toggle source

entry version number numbered by EMBL

    # File lib/bio/db/embl/embl.rb, line 476
    def entry_version
      parse_release_version(self.dt['updated'])[1]
    end

features() click to toggle source
Alias for: ft
fh() click to toggle source

returns feature table header (String) in the feature header (FH) line.

FH Line; feature table header (0 or 2)

    # File lib/bio/db/embl/embl.rb, line 325
    def fh
      fetch('FH')
    end

ft() click to toggle source

returns contents in the feature table (FT) lines.

- Bio::EMBL#ft -> Bio::Features

- Bio::EMBL#ft {} -> {|Bio::Feature| }

same as features method in bio/db/genbank.rb

FT Line; feature table data (>=0)

    # File lib/bio/db/embl/embl.rb, line 336
    def ft
      unless @data['FT']
        ary = Array.new
        in_quote = false
        @orig['FT'].each_line do |line|
          next if line =~ /^FEATURES/

          head = line[0,20].strip  # feature key (source, CDS, ...)
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
            ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
            ary.last.push(body)    # /q="data..., /q=data, /q

            if body =~ /=" / and body !~ /"$/
              in_quote = true
            end

          else
            ary.last.last << body # ...data..., ...data..."

            if body =~ /"$/
              in_quote = false
            end
          end
        end

        ary.map! do |subary|
          parse_qualifiers(subary)
        end

        @data['FT'] = ary.extend(Bio::Features::BackwardCompatibility)
      end
      if block_given?
        @data['FT'].each do |feature|
          yield feature
        end
      else
        @data['FT']
      end
    end

Also aliased as: features
id_line(key=nil) click to toggle source

returns contents in the ID line.

- Bio::EMBL#id_line -> <ID Hash>

where <ID Hash> is:

    {'ENTRY_NAME' => String, 'MOLECULE_TYPE' => String, 'DIVISION' => String,
     'SEQUENCE_LENGTH' => Int, 'SEQUENCE_VERSION' => Int}

ID Line

    "ID  ENTRY_NAME DATA_CLASS; MOLECULE_TYPE; DIVISION; SEQUENCE_LENGTH BP."

DATA_CLASS = ['standard']

MOLECULE_TYPE: DNA RNA XXX

Code ( DIVISION )

    EST (ESTs)
    PHG (Bacteriophage)
    FUN (Fungi)
    GSS (Genome survey)
    HTC (High Throughput cDNAs)
    HTG (HTGs)
    HUM (Human)
    INV (Invertebrates)
    ORG (Organelles)
    MAM (Other Mammals)
    VRT (Other Vertebrates)
    PLN (Plants)
    PRO (Prokaryotes)
    ROD (Rodents)
    SYN (Synthetic)
    STS (STSs)
    UNC (Unclassified)
    VRL (Viruses)

Rel 89- ID CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP. ID <1>; SV <2>; <3>; <4>; <5>; <6>; <7> BP.

1. Primary accession number

2. Sequence version number

3. Topology: 'circular' or 'linear'

4. Molecule type (see note 1 below)

5. Data class (see section 3.1)

6. Taxonomic division (see section 3.2)

7. Sequence length (see note 2 below)

    # File lib/bio/db/embl/embl.rb, line 89
    def id_line(key=nil)
      unless @data['ID']
        tmp = Hash.new
        idline = fetch('ID').split(/; +/)
        tmp['ENTRY_NAME'], tmp['DATA_CLASS'] = idline.shift.split(/ +/)
        if idline.first =~ /^SV/
          tmp['SEQUENCE_VERSION'] = idline.shift.split(' ').last
          tmp['TOPOLOGY'] = idline.shift
          tmp['MOLECULE_TYPE'] = idline.shift
          tmp['DATA_CLASS'] = idline.shift
        else
          tmp['MOLECULE_TYPE'] = idline.shift
        end
        tmp['DIVISION'] = idline.shift
        tmp['SEQUENCE_LENGTH'] = idline.shift.strip.split(' ').first.to_i

        @data['ID'] = tmp
      end

      if key
        @data['ID'][key]
      else
        @data['ID']
      end
    end

molecule() click to toggle source

returns MOLECULE_TYPE in the ID line.

- Bio::EMBL#molecule -> String

    # File lib/bio/db/embl/embl.rb, line 125
    def molecule
      id_line('MOLECULE_TYPE')
    end

Also aliased as: molecule_type
molecule_type() click to toggle source
Alias for: molecule
naseq() click to toggle source
Alias for: seq
ntseq() click to toggle source
Alias for: seq
os(num = nil) click to toggle source

returns contents in the OS line.

- Bio::EMBL#os -> Array of <OS Hash>

where <OS Hash> is:

    [{'name'=>'Human', 'os'=>'Homo sapiens'},
     {'name'=>'Rat', 'os'=>'Rattus norveticus'}]

- Bio::EMBL#os['name'] => "Human"

- Bio::EMBL#os => {'name'=>"Human", 'os'=>'Homo sapiens'}

OS Line; organism species (>=1)

    OS   Trifolium repens (white clover)

Typically, OS line shows "Genus species (name)" style:

    OS   Genus species (name)

Other examples:

    OS   uncultured bacterium
    OS   xxxxxx metagenome
    OS   Cloning vector xxxxxxxx

Complicated examples:

    OS   Poeciliopsis gracilis (Poeciliopsis gracilis (Heckel, 1848))
    OS   Etmopterus sp. B Last & Stevens, 1994 (bristled lanternshark)
    OS   Galaxias sp. D (Allibone et al., 1996) (Pool Burn galaxias)
    OS   Sicydiinae sp. 'Keith et al., 2010'
    OS   Acanthopagrus sp. 'Jean & Lee, 2008'
    OS   Gaussia princeps (T. Scott, 1894)
    OS   Rana sp. 8 Hillis & Wilcox, 2005
    OS   Contracaecum rudolphii C D'Amelio et al., 2007
    OS   Partula sp. 'Mt. Marau, Tahiti'
    OS   Leptocephalus sp. 'type II larva' (Smith, 1989)
    OS   Tayloria grandis (D.G.Long) Goffinet & A.J.Shaw, 2002
    OS   Non-A, non-B hepatitis virus
    OS   Canidae (dog, coyote, wolf, fox)
    OS   Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
    OS   Yersinia enterocolitica (type O:5,27)
    OS   Influenza A virus (A/green-winged teal/OH/72/99(H6N1,4))
    OS   Influenza A virus (A/Beijing/352/1989,(highgrowth reassortant NIB26)(H3N2))
    OS   Recombinant Hepatitis C virus H77(5'UTR-NS2)/JFH1_V787A,Q1247L

    # File lib/bio/db/embl/embl.rb, line 266
    def os(num = nil)
      unless @data['OS']
        os = Array.new
        tmp = fetch('OS')
        if /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d]) *\(([\w\d ]+)\)\s*\z/ =~ tmp
          org = $1
          os.push({'name' => $2, 'os' => $1})
        else
          os.push({'name' => nil, 'os' => tmp})
        end
        @data['OS'] = os
      end
      if num
        # EX. "Trifolium repens (white clover)"
        "#{@data['OS'][num]['os']} {#data['OS'][num]['name']"
      end
      @data['OS']
    end

release_created() click to toggle source

release number when created

    # File lib/bio/db/embl/embl.rb, line 471
    def release_created
      parse_release_version(self.dt['created'])[0]
    end

release_modified() click to toggle source

release number when last updated

    # File lib/bio/db/embl/embl.rb, line 466
    def release_modified
      parse_release_version(self.dt['updated'])[0]
    end

seq() click to toggle source

returns the nucleotie sequence in this entry.

- Bio::EMBL#seq -> Bio::Sequence::NA

@orig as sequence bb Line; (blanks) sequence data (>=1)

    # File lib/bio/db/embl/embl.rb, line 445
    def seq
      Bio::Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
    end

Also aliased as: naseq, ntseq
seqlen() click to toggle source
Alias for: sequence_length
sequence_length() click to toggle source

returns SEQUENCE_LENGTH in the ID line.

- Bio::EMBL#sequencelength -> String

    # File lib/bio/db/embl/embl.rb, line 146
    def sequence_length
      id_line('SEQUENCE_LENGTH')
    end

Also aliased as: seqlen
species() click to toggle source

species

    # File lib/bio/db/embl/embl.rb, line 518
    def species
      self.fetch('OS')
    end

sq(base = nil) click to toggle source

returns sequence header information in the sequence header (SQ) line.

- Bio::EMBL#sq -> <SQ Hash>

where <SQ Hash> is:

    {'ntlen' => Int, 'other' => Int,
     'a' => Int, 'c' => Int, 'g' => Int, 't' => Int}

- Bio::EMBL#sq(base) -> <base content in Int>

- Bio::EMBL#sq -> <base content in Int>

SQ Line; sequence header (1/entry)

    SQ   Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;

    # File lib/bio/db/embl/embl.rb, line 422
    def sq(base = nil)
      unless @data['SQ']
        fetch('SQ') =~               /(\d+) BP\; (\d+) A; (\d+) C; (\d+) G; (\d+) T; (\d+) other;/
        @data['SQ'] = {'ntlen' => $1.to_i, 'other' => $6.to_i,
                       'a' => $2.to_i, 'c' => $3.to_i , 'g' => $4.to_i, 't' => $5.to_i}
      else
        @data['SQ']
      end

      if base
        @data['SQ'][base.downcase]
      else
        @data['SQ']
      end
    end

sv() click to toggle source

returns the version information in the sequence version (SV) line.

- Bio::EMBL#sv -> Accession.Version in String

- Bio::EMBL#version -> accession in Int

SV Line; sequence version (1/entry)

    SV    Accession.Version

    # File lib/bio/db/embl/embl.rb, line 162
    def sv
      if (v = field_fetch('SV').sub(/;/,'')) == ""
        [id_line['ENTRY_NAME'], id_line['SEQUENCE_VERSION']].join('.')
      else
        v
      end
    end

to_biosequence() click to toggle source

converts the entry to Bio::Sequence object

Arguments |
Returns | Bio::Sequence object

    # File lib/bio/db/embl/embl.rb, line 530
    def to_biosequence
      Bio::Sequence.adapter(self, Bio::Sequence::Adapter::EMBL)
    end

topology() click to toggle source

    # File lib/bio/db/embl/embl.rb, line 134
    def topology
      id_line('TOPOLOGY')
    end

version() click to toggle source

    # File lib/bio/db/embl/embl.rb, line 169
    def version
      (sv.split(".")[1] || id_line['SEQUENCE_VERSION']).to_i
    end

[Validate]

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