### Home Classes Methods

### In Files

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

### Parent

EMBLDB

### Methods

- #aalen
- #aaseq
- #cc
- #dr
- #dt
- #embl_dr
- #entry
- #entry_id
- #entry_name
- #ft
- #gene_name
- #gene_names
- #gn
- #hi
- #id_line
- #molecule
- #molecule_type
- #oh
- #os
- #ox
- #protein_name
- #ref
- #references
- #seq
- #sequence_length
- #set_RN
- #sq
- #synonyms

### Included Modules

- Bio::EMBLDB::Common

### 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::SPTR

Parser class for UniProtKB/SwissProt and TrEMBL database entry.

### Public Instance Methods

aalen() click to toggle source
Alias for: sequence_length
aaseq() click to toggle source
Alias for: seq
cc(topic = nil) click to toggle source

returns contents in the CC lines.

- Bio::SPTR#cc -> Hash

returns an object of contents in the TOPIC.

- Bio::SPTR#cc(TOPIC) -> Array w/in Hash, Hash

returns contents of the "ALTERNATIVE PRODUCTS".

- Bio::SPTR#cc('ALTERNATIVE PRODUCTS') -> Hash

      {'Event' => str,
       'Named isoforms' => int,
       'Comment' => str,
       'Variants'=>[{'Name' => str, 'Synonyms' => str, 'IsoId' => str, 'Sequence' => []}]}

      CC   -!- ALTERNATIVE PRODUCTS:
      CC       Event=Alternative splicing; Named isoforms=15;
      ...
      CC         placentae isoforms. All tissues differentially splice exon 13;
      CC       Name=A; Synonyms=no del;
      CC         IsoId=P15529-1; Sequence=Displayed;

returns contents of the "DATABASE".

- Bio::SPTR#cc('DATABASE') -> Array

      [{'NAME'=>str,'NOTE'=>str, 'WWW'=>URI,'FTP'=>URI}, ...]

      CC   -!- DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].

returns contents of the "MASS SPECTROMETRY".

- Bio::SPTR#cc('MASS SPECTROMETRY') -> Array

      [{'MW"=>float,'MW_ERR'=>float, 'METHOD'=>str,'RANGE'=>str}, ...]

      CC   -!- MASS SPECTROMETRY: MW=XXX[; MW_ERR=XX][; METHOD=XX][;RANGE=XX-XX].

### CC lines (>=0, optional)

    CC   -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
    CC       IN LIVER, KIDNEY, LUNG AND BRAIN.

    CC   -!- TOPIC: FIRST LINE OF A COMMENT BLOCK;
    CC       SECOND AND SUBSEQUENT LINES OF A COMMENT BLOCK.

See also www.expasy.org/sprot/userman.html#CC_line

    # File lib/bio/db/embl/sptr.rb, line 775
    def cc(topic = nil)
      unless @data['CC']
        cc  = Hash.new
        comment_border= '-' * (77 - 4 + 1)
        dlm = /-!- /

        # 12KD_MYCSM has no CC lines.
        return cc if get('CC').size == 0

        cc_raw = fetch('CC')

        # Removing the copyright statement.
        cc_raw.sub!(/ *---.+---/, '')

        # Not any CC Lines without the copyright statement.
        return cc if cc_raw == ''

        begin
          cc_raw, copyright = cc_raw.split(/#{comment_border}/)[0]
          cc_raw = cc_raw.sub(dlm,'')
          cc_raw.split(dlm).each do |tmp|
            tmp = tmp.strip

            if /(^[A-Z ]+[A-Z]): (.+)/ =~ tmp
              key  = $1
              body = $2
              body.gsub!(/- (?!AND)/,'-')
              body.strip!
              unless cc[key]
                cc[key] = [body]
              else
                cc[key].push(body)
              end
            else
              raise ["Error: [#{entry_id}]: CC Lines", '"', tmp, '"',
                     '', get('CC'),''].join("\n")
            end
          end
        rescue NameError
          if fetch('CC') == ''
            return {}
          else
            raise ["Error: Invalid CC Lines: [#{entry_id}]: ",
                   "\n'#{self.get('CC')}'\n", "(#{$!})"].join
          end
        rescue NoMethodError
        end

        @data['CC'] = cc
      end

      case topic
      when 'ALLERGEN'
        return @data['CC'][topic]
      when 'ALTERNATIVE PRODUCTS'
        return cc_alternative_products(@data['CC'][topic])
      when 'BIOPHYSICOCHEMICAL PROPERTIES'
        return cc_biophysiochemical_properties(@data['CC'][topic])
      when 'BIOTECHNOLOGY'
        return @data['CC'][topic]
      when 'CATALITIC ACTIVITY'
        return cc_catalytic_activity(@data['CC'][topic])
      when 'CAUTION'
        return cc_caution(@data['CC'][topic])
      when 'COFACTOR'
        return @data['CC'][topic]
      when 'DEVELOPMENTAL STAGE'
        return @data['CC'][topic].join('')
      when 'DISEASE'
        return @data['CC'][topic].join('')
      when 'DOMAIN'
        return @data['CC'][topic]
      when 'ENZYME REGULATION'
        return @data['CC'][topic].join('')
      when 'FUNCTION'
        return @data['CC'][topic].join('')
      when 'INDUCTION'
        return @data['CC'][topic].join('')
      when 'INTERACTION'
        return cc_interaction(@data['CC'][topic])
      when 'MASS SPECTROMETRY'
        return cc_mass_spectrometry(@data['CC'][topic])
      when 'MISCELLANEOUS'
        return @data['CC'][topic]
      when 'PATHWAY'
        return cc_pathway(@data['CC'][topic])
      when 'PHARMACEUTICAL'
        return @data['CC'][topic]
      when 'POLYMORPHISM'
        return @data['CC'][topic]
      when 'PTM'
        return @data['CC'][topic]
      when 'RNA EDITING'
        return cc_rna_editing(@data['CC'][topic])
      when 'SIMILARITY'
        return @data['CC'][topic]
      when 'SUBCELLULAR LOCATION'
        return cc_subcellular_location(@data['CC'][topic])
      when 'SUBUNIT'
        return @data['CC'][topic]
      when 'TISSUE SPECIFICITY'
        return @data['CC'][topic]
      when 'TOXIC DOSE'
        return @data['CC'][topic]
      when 'WEB RESOURCE'
        return cc_web_resource(@data['CC'][topic])
      when 'DATABASE'
        # DATABASE: NAME=Text[; NOTE=Text][; WWW="Address"][; FTP="Address"].
        tmp = Array.new
        db = @data['CC']['DATABASE']
        return db unless db

        db.each do |e|
          db = {'NAME' => nil, 'NOTE' => nil, 'WWW' => nil, 'FTP' => nil}
          e.sub(/.$/,'').split(/;/).each do |line|
            case line
            when /NAME=(.+)/
              db['NAME'] = $1
            when /NOTE=(.+)/
              db['NOTE'] = $1
            when /WWW="(.+)"/
              db['WWW'] = $1
            when /FTP="(.+)"/
              db['FTP'] = $1
            end
          end
          tmp.push(db)
        end
        return tmp
      when nil
        return @data['CC']
      else
        return @data['CC'][topic]
      end
    end

dr(key = nil) click to toggle source

Bio::SPTR#dr

    # File lib/bio/db/embl/sptr.rb, line 1131
    def dr(key = nil)
      unless key
        embl_dr
      else
        (embl_dr[key] or []).map {|x|
          {'Accession' => x[0],
           'Version' => x[1],
           ' ' => x[2],
           'Molecular Type' => x[3]}
        }
      end
    end

Also aliased as: embl_dr
dt(key = nil) click to toggle source

returns a Hash of information in the DT lines.

    hash keys:
      ['created', 'sequence', 'annotation']

Since UniProtKB release 7.0 of 07-Feb-2006, the DT line format is changed, and the word "annotation" is no longer used in DT lines. Despite the change, the word "annotation" is still used for keeping compatibility.

returns a String of information in the DT lines by a given key.

### DT Line; date (3/entry)

    DT DD-MMM-YYY (integrated into UniProtKB/XXXXX.)
    DT DD-MMM-YYY (sequence version NN)
    DT DD-MMM-YYY (entry version NN)

The format have been changed in UniProtKB release 7.0 of 07-Feb-2006. Below is the older format.

### Old format of DT Line; date (3/entry)

    DT DD-MMM-YYY (rel. NN, Created)
    DT DD-MMM-YYY (rel. NN, Last sequence update)
    DT DD-MMM-YYY (rel. NN, Last annotation update)

    # File lib/bio/db/embl/sptr.rb, line 158
    def dt(key = nil)
      return dt[key] if key
      return @data['DT'] if @data['DT']

      part = self.get('DT').split(/\n/)
      @data['DT'] = {
        'created'    => part[0].sub(/\w{2}   /,'').strip,
        'sequence'   => part[1].sub(/\w{2}   /,'').strip,
        'annotation' => part[2].sub(/\w{2}   /,'').strip
      }
    end

embl_dr(key = nil) click to toggle source

Backup Bio::EMBLDB#dr as embl_dr

Alias for: dr
entry() click to toggle source
Alias for: entry_id
entry_id() click to toggle source

returns a ENTRY_NAME in the ID line.

    # File lib/bio/db/embl/sptr.rb, line 99
    def entry_id
      id_line('ENTRY_NAME')
    end

Also aliased as: entry_name, entry
entry_name() click to toggle source
Alias for: entry_id
ft(feature_key = nil) click to toggle source

returns contents in the feature table.

## Examples

    sp = Bio::SPTR.new(entry)
    ft = sp.ft
    ft.class #=> Hash
    ft.keys.each do |feature_key|
      ft[feature_key].each do |feature|
        feature['From'] #=> '1'
        feature['To']   #=> '21'
        feature['Description'] #=> ''
        feature['FTId'] #=> ''
        feature['diff'] #=> []
        feature['original'] #=> [feature_key, '1', '21', '', '']
      end
    end

- Bio::SPTR#ft -> Hash

      {FEATURE_KEY => [{'From' => int, 'To' => int,
                        'Description' => aStr, 'FTId' => aStr,
                        'diff' => [original_residues, changed_residues],
                        'original' => aAry }],...}

returns an Array of the information about the feature_name in the feature table.

- Bio::SPTR#ft(feature_name) -> Array of Hash

      [{'From' => str, 'To' => str, 'Description' => str, 'FTId' => str},...]

## FT Line; feature table data (>=0, optional)

    Col     Data item
    -----   -----------------
     1- 2   FT
     6-13   Feature name
    15-20   `FROM' endpoint
    22-27   `TO' endpoint
    35-75   Description (>=0 per key)
    -----   -----------------

Note: 'FROM' and 'TO' endopoints are allowed to use non-numerial charactors including '<', '>' or '?'. (c.f. '<1', '?42')

See also www.expasy.org/sprot/userman.html#FT_line

    # File lib/bio/db/embl/sptr.rb, line 1196
    def ft(feature_key = nil)
      return ft[feature_key] if feature_key
      return @data['FT'] if @data['FT']

      table = []
      begin
        get('FT').split("\n").each do |line|
          if line =~ /^FT   \w/
            feature = line.chomp.ljust(74)
            table << [feature[ 5..12].strip,   # Feature Name
                      feature[14..19].strip,   # From
                      feature[21..26].strip,   # To
                      feature[34..74].strip ]  # Description
          else
            table.last << line.chomp.sub!(/^FT +/, '')
          end
        end

        # Joining Description lines
        table = table.map { |feature|
          ftid = feature.pop if feature.last =~ /FTId=/
          if feature.size > 4
            feature = [feature[0],
                       feature[1],
                       feature[2],
                       feature[3, feature.size - 3].join(" ")]
          end
          feature << if ftid then ftid else '' end
        }

        hash = {}
        table.each do |feature|
          hash[feature[0]] = [] unless hash[feature[0]]
          hash[feature[0]] << {
            # Removing '<', '>' or '?' in FROM/TO endopoint.
            'From' => feature[1].sub(/\D/, '').to_i,
            'To'   => feature[2].sub(/\D/, '').to_i,
            'Description' => feature[3],
            'FTId' => feature[4].to_s.sub(/\/FTId=/, '').sub(/\.$/, ''),
            'diff' => [],
            'original' => feature
          }

          case feature[0]
          when 'VARSPLIC', 'VARIANT', 'VAR_SEQ', 'CONFLICT'
            case hash[feature[0]].last['Description']
            when /(\w[\w ]*\w*) - ?> (\w[\w ]*\w*)/
              original_res = $1
              changed_res = $2
              original_res = original_res.gsub(/ /,'').strip
              chenged_res = changed_res.gsub(/ /,'').strip
            when /Missing/
              original_res = seq.subseq(hash[feature[0]].last['From'],
                                        hash[feature[0]].last['To'])
              changed_res = ''
            end
            hash[feature[0]].last['diff'] = [original_res, chenged_res]
          end
        end
      rescue
        raise "Invalid FT Lines(#{$!}) in #{entry_id}:, \n'#{self.get('FT')}'\n"
      end

      @data['FT'] = hash
    end

gene_name() click to toggle source

returns a String of the first gene name in the GN line.

    # File lib/bio/db/embl/sptr.rb, line 438
    def gene_name
      gene_names.first
    end

gene_names() click to toggle source

returns a Array of gene names in the GN line.

    # File lib/bio/db/embl/sptr.rb, line 427
    def gene_names
      gn # set @data['GN'] if it hasn't been already done
      if @data['GN'].first.class == Hash then
        @data['GN'].collect { |element| element[:name] }
      else
        @data['GN'].first
      end
    end

gn() click to toggle source

returns gene names in the GN line.

New UniProt/SwissProt format:

- Bio::SPTR#gn -> [ <gene record>* ]

where <gene record> is:

    { :name => '...',
      :synonyms => [ 's1', 's2', ... ],
      :loci   => [ 'l1', 'l2', ... ],
      :orfs     => [ 'o1', 'o2', ... ]
    }

Old format:

- Bio::SPTR#gn -> Array # AND

- Bio::SPTR#gn -> Array # OR

### GN Line: Gene name(s) (>=0, optional)

    # File lib/bio/db/embl/sptr.rb, line 351
    def gn
      unless @data['GN']
        case fetch('GN')
        when /Name=/,/ORFNames=/,/OrderedLocusNames=/,/Synonyms=/
          @data['GN'] = gn_uniprot_parser
        else
          @data['GN'] = gn_old_parser
        end
      end
      @data['GN']
    end

hi() click to toggle source

### The HI line

Bio::SPTR#hi #=> hash

    # File lib/bio/db/embl/sptr.rb, line 691
    def hi
      unless @data['HI']
        @data['HI'] = []
        fetch('HI').split(/\. /).each do |hlist|
          hash = {'Category' => '',  'Keywords' => [], 'Keyword' => ''}
          hash['Category'], hash['Keywords'] = hlist.split(': ')
          hash['Keywords'] = hash['Keywords'].split('; ')
          hash['Keyword'] = hash['Keywords'].pop
          hash['Keyword'].sub!(/\.$/, '')
          @data['HI'] << hash
        end
      end
      @data['HI']
    end

id_line(key = nil) click to toggle source

returns a Hash of the ID line.

returns a content (Int or String) of the ID line by a given key. Hash keys: ['ENTRY_NAME', 'DATA_CLASS', 'MODECULE_TYPE', 'SEQUENCE_LENGTH']

### ID Line (since UniProtKB release 9.0 of 31-Oct-2006)

    ID   P53_HUMAN               Reviewed;         393 AA.
    #"ID  #{ENTRY_NAME} #{DATA_CLASS}; #{SEQUENCE_LENGTH}."

### Examples

    obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"Reviewed",
                      "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>nil}

    obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"

### ID Line (older style)

    ID   P53_HUMAN      STANDARD;      PRT;   393 AA.
    #"ID  #{ENTRY_NAME} #{DATA_CLASS}; #{MOLECULE_TYPE}; #{SEQUENCE_LENGTH}."

### Examples

    obj.id_line  #=> {"ENTRY_NAME"=>"P53_HUMAN", "DATA_CLASS"=>"STANDARD",
                      "SEQUENCE_LENGTH"=>393, "MOLECULE_TYPE"=>"PRT"}

    obj.id_line('ENTRY_NAME') #=> "P53_HUMAN"

    # File lib/bio/db/embl/sptr.rb, line 74
    def id_line(key = nil)
      return id_line[key] if key
      return @data['ID'] if @data['ID']

      part = @orig['ID'].split(/ +/)
      if part[4].to_s.chomp == 'AA.' then
        # after UniProtKB release 9.0 of 31-Oct-2006
        # (http://www.uniprot.org/docs/sp_news.htm)
        molecule_type   = nil
        sequence_length = part[3].to_i
      else
        molecule_type   = part[3].sub(/;/,'')
        sequence_length = part[4].to_i
      end
      @data['ID'] = {
        'ENTRY_NAME'      => part[1],
        'DATA_CLASS'      => part[2].sub(/;/,''),
        'MOLECULE_TYPE'   => molecule_type,
        'SEQUENCE_LENGTH' => sequence_length
      }
    end

molecule() click to toggle source

returns a MOLECULE_TYPE in the ID line.

A short-cut for Bio::SPTR#id_line('MOLECULE_TYPE').

    # File lib/bio/db/embl/sptr.rb, line 109
    def molecule
      id_line('MOLECULE_TYPE')
    end

Also aliased as: molecule_type
molecule_type() click to toggle source
Alias for: molecule
oh() click to toggle source

### The OH Line;

OH NCBI_TaxID=TaxID; HostName. br.expasy.org/sprot/userman.html#OH_line

    # File lib/bio/db/embl/sptr.rb, line 521
    def oh
      unless @data['OH']
        @data['OH'] = fetch('OH').split("\. ").map {|x|
          if x =~ /NCBI_TaxID=(\d+);/
            taxid = $1
          else
            raise ArgumentError, ["Error: Invalid OH line format (#{self.entry_id}):",
                                  $!, "\n", get('OH'), "\n"].join

          end
          if x =~ /NCBI_TaxID=\d+; (.+)/
            host_name = $1
            host_name.sub!(/\.$/, '')
          else
            host_name = nil
          end
          {'NCBI_TaxID' => taxid, 'HostName' => host_name}
        }
      end
      @data['OH']
    end

os(num = nil) click to toggle source

returns a Array of Hashs or a String of the OS line when a key given.

- Bio::EMBLDB#os -> Array

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

- Bio::EPTR#os -> Hash

    {'name' => "(Human)", 'os' => 'Homo sapiens'}

- Bio::SPTR#os['name'] -> "(Human)"

- Bio::EPTR#os(0) -> "Homo sapiens (Human)"

### OS Line; organism species (>=1)

    OS   Genus species (name).
    OS   Genus species (name0) (name1).
    OS   Genus species (name0) (name1).
    OS   Genus species (name0), G s0 (name0), and G s (name0) (name1).
    OS   Homo sapiens (Human), and Rarrus norveticus (Rat)
    OS   Hippotis sp. Clark and Watts 825.
    OS   unknown cyperaceous sp.

    # File lib/bio/db/embl/sptr.rb, line 460
    def os(num = nil)
      unless @data['OS']
        os = Array.new
        fetch('OS').split(/, and|, /).each do |tmp|
          if tmp =~ /(\w+ *[\w\d \:\'\+\-\.]+[\w\d\.])/
            org = $1
            tmp =~ /(\(.+\))/
            os.push({'name' => $1, 'os' => org})
          else
            raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n"
          end
        end
        @data['OS'] = os
      end

      if num
        # EX. "Trifolium repens (white clover)"
        return "#{@data['OS'][num]['os']} #{@data['OS'][num]['name']}"
      else
        return @data['OS']
      end
    end

ox() click to toggle source

returns a Hash of oraganism taxonomy cross-references.

- Bio::SPTR#ox -> Hash

      {'NCBI_TaxID' => ['1234','2345','3456','4567'], ...}

### OX Line; organism taxonomy cross-reference (>=1 per entry)

    OX   NCBI_TaxID=1234;
    OX   NCBI_TaxID=1234, 2345, 3456, 4567;

    # File lib/bio/db/embl/sptr.rb, line 504
    def ox
      unless @data['OX']
        tmp = fetch('OX').sub(/\.$/,'').split(/;/).map { |e| e.strip }
        hsh = Hash.new
        tmp.each do |e|
          db,refs = e.split(/=/)
          hsh[db] = refs.split(/, */)
        end
        @data['OX'] = hsh
      end
      return @data['OX']
    end

protein_name() click to toggle source

returns the proposed official name of the protein. Returns a String.

Since UniProtKB release 14.0 of 22-Jul-2008, the DE line format have been changed. The method returns the full name which is taken from "RecName: Full=" or "SubName: Full=" line normally in the beginning of the DE lines. Unlike parser for old format, no special treatments for fragment or precursor.

For old format, the method parses the DE lines and returns the protein name as a String.

### DE Line; description (>=1)

    "DE #{OFFICIAL_NAME} (#{SYNONYM})"
    "DE #{OFFICIAL_NAME} (#{SYNONYM}) [CONTEINS: #1; #2]."
    OFFICIAL_NAME  1/entry
    SYNONYM        >=0
    CONTEINS       >=0

    # File lib/bio/db/embl/sptr.rb, line 251
    def protein_name
      @data['DE'] ||= parse_DE_line_rel14(get('DE'))
      parsed_de_line = @data['DE']
      if parsed_de_line then
        # since UniProtKB release 14.0 of 22-Jul-2008
        name = nil
        parsed_de_line.each do |a|
          case a[0]
          when 'RecName', 'SubName'
            if name_pair = a[1..-1].find { |b| b[0] == 'Full' } then
              name = name_pair[1]
              break
            end
          end
        end
        name = name.to_s
      else
        # old format (before Rel. 13.x)
        name = ""
        if de_line = fetch('DE') then
          str = de_line[/^[^\[]*/] # everything preceding the first [ (the "contains" part)
          name = str[/^[^(]*/].strip
          name << ' (Fragment)' if str =~ /fragment/
        end
      end
      return name
    end

ref() click to toggle source

returns contents in the R lines.

- Bio::EMBLDB::Common#ref -> [ <refernece information Hash>* ]

where <reference information Hash> is:

    {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '',
     'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}

R Lines

- RN RC RP RX RA RT RL RG

    # File lib/bio/db/embl/sptr.rb, line 557
    def ref
      unless @data['R']
        @data['R'] = [get('R').split(/\nRN   /)].flatten.map { |str|
          hash = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '',
                 'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
          str = 'RN   ' + str unless /^RN   / =~ str

          str.split("\n").each do |line|
            if /^(R[NPXARLCTG])   (.+)/ =~ line
              hash[$1] += $2 + ' '
            else
              raise "Invalid format in R lines, \n[#{line}]\n"
            end
          end

          hash['RN'] = set_RN(hash['RN'])
          hash['RC'] = set_RC(hash['RC'])
          hash['RP'] = set_RP(hash['RP'])
          hash['RX'] = set_RX(hash['RX'])
          hash['RA'] = set_RA(hash['RA'])
          hash['RT'] = set_RT(hash['RT'])
          hash['RL'] = set_RL(hash['RL'])
          hash['RG'] = set_RG(hash['RG'])

          hash
        }

      end
      @data['R']
    end

references() click to toggle source

returns Bio::Reference object from Bio::EMBLDB::Common#ref.

- Bio::EMBLDB::Common#ref -> Bio::References

    # File lib/bio/db/embl/sptr.rb, line 651
    def references
      unless @data['references']
        ary = self.ref.map {|ent|
          hash = Hash.new('')
          ent.each {|key, value|
            case key
            when 'RA'
              hash['authors'] = value.split(/, /)
            when 'RT'
              hash['title'] = value
            when 'RL'
              if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
                hash['journal'] = $1
                hash['volume']  = $2
                hash['issue']   = $3
                hash['pages']   = $4
                hash['year']    = $5
              else
                hash['journal'] = value
              end
            when 'RX'  # PUBMED, MEDLINE, DOI
              value.each do |tag, xref|
                hash[ tag.downcase ]  = xref
              end
            end
          }
          Reference.new(hash)
        }
        @data['references'] = References.new(ary)
      end
      @data['references']
    end

seq() click to toggle source

returns a Bio::Sequence::AA of the amino acid sequence.

- Bio::SPTR#seq -> Bio::Sequence::AA

blank Line; sequence data (>=1)

    # File lib/bio/db/embl/sptr.rb, line 1306
    def seq
      unless @data['']
        @data[''] = Sequence::AA.new( fetch('').gsub(/ |\d+/,'') )
      end
      return @data['']
    end

Also aliased as: aaseq
sequence_length() click to toggle source

returns a SEQUENCE_LENGTH in the ID line.

A short-cut for Bio::SPTR#id_line('SEQUENCE_LENGHT').

    # File lib/bio/db/embl/sptr.rb, line 118
    def sequence_length
      id_line('SEQUENCE_LENGTH')
    end

Also aliased as: aalen
set_RN(data) click to toggle source

    # File lib/bio/db/embl/sptr.rb, line 588
    def set_RN(data)
      data.strip
    end

sq(key = nil) click to toggle source

returns a Hash of conteins in the SQ lines.

- Bio::SPTRL#sq -> hsh

returns a value of a key given in the SQ lines.

- Bio::SPTRL#sq(key) -> int or str

- Keys: ['MW', 'mw', 'molecular', 'weight', 'aalen', 'len', 'length',

      'CRC64']

### SQ Line; sequence header (1/entry)

    SQ   SEQUENCE   233 AA;  25630 MW;  146A1B48A1475C86 CRC64;
    SQ   SEQUENCE  \d+ AA; \d+ MW;  [0-9A-Z]+ CRC64;

MW, Dalton unit. CRC64 (64-bit Cyclic Redundancy Check, ISO 3309).

    # File lib/bio/db/embl/sptr.rb, line 1278
    def sq(key = nil)
      unless @data['SQ']
        if fetch('SQ') =~ /(\d+) AA\; (\d+) MW; (.+) CRC64;/
          @data['SQ'] = { 'aalen' => $1.to_i, 'MW' => $2.to_i, 'CRC64' => $3 }
        else
          raise "Invalid SQ Line: \n'#{fetch('SQ')}'"
        end
      end

      if key
        case key
        when /mw/, /molecular/, /weight/
          @data['SQ']['MW']
        when /len/, /length/, /AA/
          @data['SQ']['aalen']
        else
          @data['SQ'][key]
        end
      else
        @data['SQ']
      end
    end

synonyms() click to toggle source

returns synonyms (unofficial and/or alternative names). Returns an Array containing String objects.

Since UniProtKB release 14.0 of 22-Jul-2008, the DE line format have been changed. The method returns the full or short names which are taken from "RecName: Short=", "RecName: EC=", and AltName lines, except after "Contains:" or "Includes:". For keeping compatibility with old format parser, "RecName: EC=N.N.N.N" is reported as "EC N.N.N.N". In addition, to prevent confusion, "Allergen=" and "CD_antigen=" prefixes are added for the corresponding fields.

For old format, the method parses the DE lines and returns synonyms. synonyms are each placed in () following the official name on the DE line.

    # File lib/bio/db/embl/sptr.rb, line 294
    def synonyms
      ary = Array.new
      @data['DE'] ||= parse_DE_line_rel14(get('DE'))
      parsed_de_line = @data['DE']
      if parsed_de_line then
        # since UniProtKB release 14.0 of 22-Jul-2008
        parsed_de_line.each do |a|
          case a[0]
          when 'Includes', 'Contains'
            break #the each loop
          when 'RecName', 'SubName', 'AltName'
            a[1..-1].each do |b|
              if name = b[1] and b[1] != self.protein_name then
                case b[0]
                when 'EC'
                  name = "EC " + b[1]
                when 'Allergen', 'CD_antigen'
                  name = b[0] + '=' + b[1]
                else
                  name = b[1]
                end
                ary.push name
              end
            end
          end #case a[0]
        end #parsed_de_line.each
      else
        # old format (before Rel. 13.x)
        if de_line = fetch('DE') then
          line = de_line.sub(/\[.*\]/,'') # ignore stuff between [ and ].  That's the "contains" part
        line.scan(/\([^)]+/) do |synonym|
          unless synonym =~ /fragment/ then
            ary << synonym[1..-1].strip # index to remove the leading (
          end
          end
        end
      end
      return ary
    end

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