### Home Classes Methods

### In Files

- lib/bio/db/biosql/sequence.rb

### Parent

Object

### Methods

- ::new
- #cdsfeatures
- #comment=
- #comments
- #database
- #database_desc
- #definition
- #definition=
- #delete
- #description
- #description=
- #division
- #division=
- #entry_id
- #entry_id=
- #feature=
- #features
- #get_seqfeature
- #identifier
- #identifier=
- #length
- #length=
- #name
- #name=
- #organism
- #organism=
- #other_seqids
- #primary_accession
- #primary_accession=
- #reference=
- #references
- #save
- #seq
- #seq=
- #sequence_version
- #sequence_version=
- #species
- #species=
- #taxonomy
- #to_biosequence
- #to_biosql
- #to_fasta
- #to_fasta_reverse_complememt
- #version
- #version=

### 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::SQL::Sequence

### Attributes

entry[R]

### Public Class Methods

new(options={}) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 106
    def initialize(options={})
      #options.assert_valid_keys(:entry, :biodatabase,:biosequence)
      return @entry = options[:entry] unless options[:entry].nil?

      return to_biosql(options[:biosequence], options[:biodatabase]) unless options[:biosequence].nil? or options[:biodatabase].nil?

    end

### Public Instance Methods

cdsfeatures() click to toggle source

return the seqfeature mapped from BioSQL with a type_term like 'CDS'

    # File lib/bio/db/biosql/sequence.rb, line 323
    def cdsfeatures
      @entry.cdsfeatures
    end

comment=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 420
    def comment=(value)
      #DELETE        comment=Comment.new({:bioentry=>@entry, :comment_text=>value, :rank=>@entry.comments.count.succ})
      comment = @entry.comments.build({:comment_text=>value, :rank=>@entry.comments.count.succ})
      comment.save
    end

comments() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 393
    def comments
      @entry.comments.map do |comment|
        comment.comment_text
      end
    end

database() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 234
    def database
      @entry.biodatabase.name
    end

database_desc() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 238
    def database_desc
      @entry.biodatabase.description
    end

definition() click to toggle source
Alias for: description
definition=(value) click to toggle source
Alias for: description=
delete() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 85
    def delete
      #TODO: check is references connected to this bioentry are leaf or not.
      #actually I think it should be more sofisticated, check if there are
      #other bioentries connected to references; if not delete 'em
      @entry.references.each { |ref| ref.delete if ref.bioentries.size==1}
      @entry.destroy
    end

description() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 260
    def description
      @entry.description
    end

Also aliased as: definition
description=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 265
    def description=(value)
      @entry.description=value
    end

Also aliased as: definition=
division() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 252
    def division
      @entry.division
    end

division=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 256
    def division=(value)
      @entry.division=value
    end

entry_id() click to toggle source
Alias for: name
entry_id=(value) click to toggle source
Alias for: name=
feature=(feat) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 293
    def feature=(feat)
      #ToDo: avoid Ontology find here, probably more efficient create class variables
      #DELETE        type_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Keys'})
      puts "feature:type_term = #{feat.feature}" if $DEBUG
      type_term = Term.first(:conditions=>["name = ?", feat.feature]) || Term.create({:name=>feat.feature, :ontology=>Ontology.first(:conditions=>["name = ?",'SeqFeature Keys'])})
      #DELETE        source_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Sources'})
      puts "feature:source_term" if $DEBUG
      source_term = Term.first(:conditions=>["name = ?",'EMBLGenBankSwit'])
      puts "feature:seqfeature" if $DEBUG
      seqfeature = @entry.seqfeatures.build({:source_term=>source_term, :type_term=>type_term, :rank=>@entry.seqfeatures.count.succ, :display_name=>''})
      seqfeature.save
      puts "feature:location" if $DEBUG
      feat.locations.each do |loc|
        location = seqfeature.locations.build({:seqfeature=>seqfeature, :start_pos=>loc.from, :end_pos=>loc.to, :strand=>loc.strand, :rank=>seqfeature.locations.count.succ})
        location.save
      end

      #DELETE        qual_term_ontology = Ontology.find_or_create({:name=>'Annotation Tags'})

      puts "feature:qualifier" if $DEBUG
      feat.each do |qualifier|
        #DELETE          qual_term = Term.find_or_create({:name=>qualifier.qualifier}, {:ontology=>qual_term_ontology})
        qual_term = Term.first(:conditions=>["name = ?", qualifier.qualifier]) || Term.create({:name=>qualifier.qualifier, :ontology=>Ontology.first(:conditions=>["name = ?", 'Annotation Tags'])})
        qual = seqfeature.seqfeature_qualifier_values.build({:seqfeature=>seqfeature, :term=>qual_term, :value=>qualifier.value.to_s, :rank=>seqfeature.seqfeature_qualifier_values.count.succ})
        qual.save

      end
    end

features() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 287
    def features
      @entry.seqfeatures.collect do |sf|
        self.get_seqfeature(sf)
      end
    end

get_seqfeature(sf) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 93
    def get_seqfeature(sf)

      #in seqfeature BioSQL class
      locations_str = sf.locations.map{|loc| loc.to_s}.join(',')
      #pp sf.locations.inspect
      locations_str = "join(#{locations_str})" if sf.locations.count>1
      Bio::Feature.new(sf.type_term.name, locations_str,sf.seqfeature_qualifier_values.collect{|sfqv| Bio::Feature::Qualifier.new(sfqv.term.name,sfqv.value)})
    end

identifier() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 270
    def identifier
      @entry.identifier
    end

Also aliased as: other_seqids
identifier=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 275
    def identifier=(value)
      @entry.identifier=value
    end

length() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 365
    def length
      @entry.biosequence.length
    end

length=(len) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 102
    def length=(len)
      @entry.biosequence.length=len
    end

name() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 195
    def name
      @entry.name
    end

Also aliased as: entry_id
name=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 200
    def name=(value)
      @entry.name=value
    end

Also aliased as: entry_id=
organism() click to toggle source

TODO def secondary_accession

      @entry.bioentry_qualifier_values
    end

    # File lib/bio/db/biosql/sequence.rb, line 217
    def organism
      @entry.taxon.nil? ? "" : "#{@entry.taxon.taxon_scientific_name.name}"+ (@entry.taxon.taxon_genbank_common_name ? "(#{@entry.taxon.taxon_genbank_common_name.name})" : '')
    end

Also aliased as: species
organism=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 222
    def organism=(value)
      #FIX there is a shortcut
      taxon_name=TaxonName.first(:conditions=>["name = ? and name_class = ?",value.gsub(/\s+\(.+\)/,''),'scientific name'])
      if taxon_name.nil?
        puts "Error value doesn't exists in taxon_name table with scientific name constraint."
      else
        @entry.taxon_id=taxon_name.taxon_id
        @entry.save
      end
    end

Also aliased as: species=
other_seqids() click to toggle source
Alias for: identifier
primary_accession() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 205
    def primary_accession
      @entry.accession
    end

primary_accession=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 209
    def primary_accession=(value)
      @entry.accession=value
    end

reference=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 399
    def reference=(value)
      locations=Array.new
      locations << "journal=#{value.journal}" unless value.journal.empty?
      locations << "volume=#{value.volume}" unless value.volume.empty?
      locations << "issue=#{value.issue}" unless value.issue.empty?
      locations << "pages=#{value.pages}" unless value.pages.empty?
      locations << "year=#{value.year}" unless value.year.empty?
      locations << "pubmed=#{value.pubmed}" unless value.pubmed.empty?
      locations << "medline=#{value.medline}" unless value.medline.empty?
      locations << "doi=#{value.doi}" unless value.doi.nil?
      locations << "abstract=#{value.abstract}" unless value.abstract.empty?
      locations << "url=#{value.url}" unless value.url.nil?
      locations << "mesh=#{value.mesh}" unless value.mesh.empty?
      locations << "affiliations=#{value.affiliations}" unless value.affiliations.empty?
      locations << "comments=#{value.comments.join('~')}"unless value.comments.nil?
      start_pos, end_pos = value.sequence_position ? value.sequence_position.gsub(/\s*/,'').split('-') : [nil,nil]
      reference= Reference.first(:conditions=>["title = ?",value.title]) || Reference.create({:title=>value.title,:authors=>value.authors.join(' '), :location=>locations.join('|')})
      bio_reference=@entry.bioentry_references.build({:reference=>reference,:rank=>value.embl_gb_record_number, :start_pos=>start_pos, :end_pos=>end_pos})
      bio_reference.save
    end

references() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 369
    def references
      #return and array of hash, hash has these keys ["title", "dbxref_id", "reference_id", "authors", "crc", "location"]
      #probably would be better to d a class refrence to collect these informations
      @entry.bioentry_references.collect do |bio_ref|
        hash = Hash.new
        hash['authors'] = bio_ref.reference.authors.gsub(/\.\s/, "\.\s\|").split(/\|/)

        hash['sequence_position'] = "#{bio_ref.start_pos}-#{bio_ref.end_pos}" if (bio_ref.start_pos and bio_ref.end_pos)
        hash['title'] = bio_ref.reference.title
        hash['embl_gb_record_number'] = bio_ref.rank
        #TODO: solve the problem with specific comment per reference.
        #TODO: get dbxref
        #take a look when location is build up in def reference=(value)

        bio_ref.reference.location.split('|').each do |element|
          key,value=element.split('=')
          hash[key]=value
        end unless bio_ref.reference.location.nil?

        hash['xrefs'] = bio_ref.reference.dbxref ? "#{bio_ref.reference.dbxref.dbname}; #{bio_ref.reference.dbxref.accession}." : ''
        Bio::Reference.new(hash)
      end
    end

save() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 426
    def save
      #I should add chks for SQL errors
      @entry.biosequence.save
      @entry.save
    end

seq() click to toggle source

Returns the sequence. Returns a Bio::Sequence::Generic object.

    # File lib/bio/db/biosql/sequence.rb, line 330
    def seq
      s = @entry.biosequence
      Bio::Sequence::Generic.new(s ? s.seq : '')
    end

seq=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 335
    def seq=(value)
      #TODO: revise this piece of code.
      #chk which type of alphabet is, NU/NA/nil
      if @entry.biosequence.nil?
        #DELETE          puts "intoseq1"
        @entry.biosequence = Biosequence.new(:seq=>value)
        #          biosequence = @entry.biosequence.build({:seq=>value})
        @entry.biosequence.save
        #          biosequence.save
      else
        @entry.biosequence.seq=value
      end
      self.length=value.length
      #DELETE        #@entry.biosequence.length=value.length
      #DELETE        #break
      @entry.save
    end

sequence_version() click to toggle source
Alias for: version
sequence_version=(value) click to toggle source
Alias for: version=
species() click to toggle source
Alias for: organism
species=(value) click to toggle source
Alias for: organism=
taxonomy() click to toggle source

report parents and exclude info with "no rank". Now I report rank == class but ... Question ? Have to be reported taxonomy with rank=="class"?

    # File lib/bio/db/biosql/sequence.rb, line 354
    def taxonomy
      tax = []
      taxon = Taxon.first(:conditions=>["taxon_id = ?",@entry.taxon.parent_taxon_id])
      while taxon and taxon.taxon_id != taxon.parent_taxon_id and taxon.node_rank!='no rank'
        tax << taxon.taxon_scientific_name.name if taxon.node_rank!='class'
        #Note: I don't like this call very much, correct with a relationship in the ref class.
        taxon = Taxon.first(:conditions=>["taxon_id = ?",taxon.parent_taxon_id])
      end
      tax.reverse
    end

to_biosequence() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 439
    def to_biosequence
      Bio::Sequence.adapter(self,Bio::Sequence::Adapter::BioSQL)
    end

to_biosql(bs,biodatabase) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 114
    def to_biosql(bs,biodatabase)
      #DELETE        #Transcaction works greatly!!!
      begin
        #DELETE          Bioentry.transaction do
        @entry = biodatabase.bioentries.build({:name=>bs.entry_id})

        puts "primary" if $DEBUG
        self.primary_accession = bs.primary_accession

        puts "def" if $DEBUG
        self.definition = bs.definition unless bs.definition.nil?

        puts "seqver" if $DEBUG
        self.sequence_version = bs.sequence_version || 0

        puts "divi" if $DEBUG
        self.division = bs.division unless bs.division.nil?

        puts "identifier" if $DEBUG
        self.identifier = bs.other_seqids.collect{|dblink| "#{dblink.database}:#{dblink.id}"}.join(';') unless bs.other_seqids.nil?
        @entry.save
        puts "secacc" if $DEBUG

        bs.secondary_accessions.each do |sa|
          puts "#{sa}" if $DEBUG
          #write as qualifier every secondary accession into the array
          self.secondary_accessions = sa
        end unless bs.secondary_accessions.nil?

        #to create the sequence entry needs to exists
        puts "seq" if $DEBUG
        puts bs.seq if $DEBUG
        self.seq = bs.seq unless bs.seq.nil?
        puts "mol" if $DEBUG

        self.molecule_type = bs.molecule_type unless bs.molecule_type.nil?
        puts "dc" if $DEBUG

        self.data_class = bs.data_class unless bs.data_class.nil?
        puts "top" if $DEBUG
        self.topology = bs.topology unless bs.topology.nil?
        puts "datec" if $DEBUG
        self.date_created = bs.date_created unless bs.date_created.nil?
        puts "datemod" if $DEBUG
        self.date_modified = bs.date_modified unless bs.date_modified.nil?
        puts "key" if $DEBUG

        bs.keywords.each do |kw|
          #write as qualifier every secondary accessions into the array
          self.keywords = kw
        end unless bs.keywords.nil?

        puts "spec" if $DEBUG
        #self.species = bs.species unless bs.species.nil?
        self.species = bs.species unless bs.species.empty?
        puts "Debug: #{bs.species}" if $DEBUG
        puts "Debug: feat..start" if $DEBUG

        bs.features.each do |feat|
          self.feature=feat
        end unless bs.features.nil?

        puts "Debug: feat...end" if $DEBUG
        bs.references.each do |reference|
          self.reference=reference
        end unless bs.references.nil?

        bs.comments.each do |comment|
          self.comment=comment
        end unless bs.comments.nil?

        #DELETE          end #transaction
        return self
      rescue Exception => e
        puts "to_biosql exception: #{e}"
        puts $!
      end #rescue
    end

to_fasta() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 431
    def to_fasta
      ">" + accession + "\n" + seq.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
    end

to_fasta_reverse_complememt() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 435
    def to_fasta_reverse_complememt
      ">" + accession + "\n" + seq.reverse_complement.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
    end

version() click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 242
    def version
      @entry.version
    end

Also aliased as: sequence_version
version=(value) click to toggle source

    # File lib/bio/db/biosql/sequence.rb, line 247
    def version=(value)
      @entry.version=value
    end

Also aliased as: sequence_version=

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