### Home Classes Methods

### In Files

- lib/bio/db/fastq.rb

### Parent

Object

### Namespace

- CLASS Bio::Fastq::Error
- CLASS Bio::Fastq::FormatData

### Methods

- ::new
- #add_header_line
- #add_line
- #entry_id
- #error_probabilities
- #format
- #format=
- #mask
- #nalen
- #naseq
- #qualities
- #quality_score_type
- #quality_scores
- #seq
- #to_biosequence
- #to_s
- #validate_format

### 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
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- 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
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- Bio::Alignment::GAP
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- Bio::AminoAcid
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- Bio::Blat
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- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
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- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
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- Bio::DAS::TYPES
- Bio::DB
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- 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
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- Bio::EBI
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- 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
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- 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
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- Bio::Location
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- 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
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- 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
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- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
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- Bio::PAML::Baseml
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- 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
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- Bio::PAML::Yn00
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- Bio::PDB
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- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
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- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
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- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
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- 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
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- Bio::PDB::HetatmFinder
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- Bio::PDB::Record::ANISOU
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- Bio::PDB::Residue
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- 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
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- 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
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- 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
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- 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
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- Bio::Shell::Core
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- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
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- 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::Fastq

Bio::Fastq is a parser for FASTQ format.

### Constants

DefaultFormatName

  Default format name

FLATFILE_SPLITTER

  Splitter for Bio::FlatFile

FormatNames

  Available format names.

Formats

  Available format name symbols.

### Attributes

definition[R]

definition; ID line (begins with @)

entry_overrun[R]

entry_overrun

header[R]

misc lines before the entry (String or nil)

quality_string[R]

quality as a string

sequence_string[R]

raw sequence data as a String object

### Public Class Methods

new(str = nil) click to toggle source

Creates a new Fastq object from formatted text string.

The format of quality scores should be specified later by using `format=` method.

Arguments:

- str: Formatted string (String)

    # File lib/bio/db/fastq.rb, line 383
    def initialize(str = nil)
      return unless str
      sc = StringScanner.new(str)
      while !sc.eos? and line = sc.scan(/.*(?:\n|\r|\r\n)?/)
        unless add_header_line(line) then
          sc.unscan
          break
        end
      end
      while !sc.eos? and line = sc.scan(/.*(?:\n|\r|\r\n)?/)
        unless add_line(line) then
          sc.unscan
          break
        end
      end
      @entry_overrun = sc.rest
    end

### Public Instance Methods

add_header_line(line) click to toggle source

Adds a header line if the header data is not yet given and the given line is suitable for header. Returns self if adding header line is succeeded. Otherwise, returns false (the line is not added).

    # File lib/bio/db/fastq.rb, line 324
    def add_header_line(line)
      @header ||= ""
      if line[0,1] == "@" then
        false
      else
        @header.concat line
        self
      end
    end

add_line(line) click to toggle source

Adds a line to the entry if the given line is regarded as a part of the current entry.

    # File lib/bio/db/fastq.rb, line 339
    def add_line(line)
      line = line.chomp
      if !defined? @definition then
        if line[0, 1] == "@" then
          @definition = line[1..-1]
        else
          @definition = line
          @parse_errors ||= []
          @parse_errors.push Error::No_atmark.new
        end
        return self
      end
      if defined? @definition2 then
        @quality_string ||= ''
        if line[0, 1] == "@" and
            @quality_string.size >= @sequence_string.size then
          return false
        else
          @quality_string.concat line
          return self
        end
      else
        @sequence_string ||= ''
        if line[0, 1] == '+' then
          @definition2 = line[1..-1]
        else
          @sequence_string.concat line
        end
        return self
      end
      raise "Bug: should not reach here!"
    end

entry_id() click to toggle source

Identifier of the entry. Normally, the first word of the ID line.

    # File lib/bio/db/fastq.rb, line 446
    def entry_id
      unless defined? @entry_id then
        eid = @definition.strip.split(/\s+/)[0] || @definition
        @entry_id = eid
      end
      @entry_id
    end

error_probabilities() click to toggle source

Estimated probability of error for each base.

Returns | (Array containing Float) error probability values

    # File lib/bio/db/fastq.rb, line 529
    def error_probabilities
      unless defined? @error_probabilities then
        self.format ||= self.class::DefaultFormatName
        a = @format.q2p(self.quality_scores)
        @error_probabilities = a
      end
      @error_probabilities
    end

format() click to toggle source

Format name. One of "fastq-sanger", "fastq-solexa", "fastq-illumina", or nil (when not specified).

Returns | (String or nil) format name

    # File lib/bio/db/fastq.rb, line 497
    def format
      @format ? @format.name : nil
    end

format=(name) click to toggle source

Specify the format. If the format is not found, raises RuntimeError.

Available formats are:

    "fastq-sanger" or :fastq_sanger
    "fastq-solexa" or :fastq_solexa
    "fastq-illumina" or :fastq_illumina

Arguments:

- (required) name: format name (String or Symbol).

Returns | (String) format name

    # File lib/bio/db/fastq.rb, line 476
    def format=(name)
      if name then
        f = FormatNames[name] || Formats[name]
        if f then
          reset_state
          @format = f.instance
          self.format
        else
          raise "unknown format"
        end
      else
        reset_state
        nil
      end
    end

mask(threshold, mask_char = 'n') click to toggle source

Masks low quality sequence regions. For each sequence position, if the quality score is smaller than the threshold, the sequence in the position is replaced with mask_char.

Note: This method does not care quality_score_type.

Arguments:

- (required) threshold : (Numeric) threshold

- (optional) mask_char : (String) character used for masking

Returns | Bio::Sequence object

    # File lib/bio/db/fastq.rb, line 668
    def mask(threshold, mask_char = 'n')
      to_biosequence.mask_with_quality_score(threshold, mask_char)
    end

nalen() click to toggle source

length of naseq

    # File lib/bio/db/fastq.rb, line 433
    def nalen
      naseq.length
    end

naseq() click to toggle source

returns Bio::Sequence::NA

    # File lib/bio/db/fastq.rb, line 425
    def naseq
      unless defined? @naseq then
        @naseq = Bio::Sequence::NA.new(@sequence_string)
      end
      @naseq
    end

qualities() click to toggle source
Alias for: quality_scores
quality_score_type() click to toggle source

The meaning of the quality scores. It may be one of :phred, :solexa, or nil.

    # File lib/bio/db/fastq.rb, line 504
    def quality_score_type
      self.format ||= self.class::DefaultFormatName
      @format.quality_score_type
    end

quality_scores() click to toggle source

Quality score for each base. For "fastq-sanger" or "fastq-illumina", it is PHRED score. For "fastq-solexa", it is Solexa score.

Returns | (Array containing Integer) quality score values

    # File lib/bio/db/fastq.rb, line 515
    def quality_scores
      unless defined? @quality_scores then
        self.format ||= self.class::DefaultFormatName
        s = @format.str2scores(@quality_string)
        @quality_scores = s
      end
      @quality_scores
    end

Also aliased as: qualities
seq() click to toggle source

returns Bio::Sequence::Generic

    # File lib/bio/db/fastq.rb, line 438
    def seq
      unless defined? @seq then
        @seq = Bio::Sequence::Generic.new(@sequence_string)
      end
      @seq
    end

to_biosequence() click to toggle source

Returns sequence as a Bio::Sequence object.

Note: If you modify the returned Bio::Sequence object, the sequence or definition in this Fastq object might also be changed (but not always be changed) because of efficiency.

    # File lib/bio/db/fastq.rb, line 653
    def to_biosequence
      Bio::Sequence.adapter(self, Bio::Sequence::Adapter::Fastq)
    end

to_s() click to toggle source

Returns Fastq formatted string constructed from instance variables. The string will always be consisted of four lines without wrapping of the sequence and quality string, and the third-line is always only contains "+". This may be different from initial entry.

Note that use of the method may be inefficient and may lose performance because new string object is created every time it is called. For showing an entry as-is, consider using Bio::FlatFile#entry_raw. For output with various options, use Bio::Sequence#output(:fastq).

    # File lib/bio/db/fastq.rb, line 420
    def to_s
      "@#{@definition}\n#{@sequence_string}\n+\n#{@quality_string}\n"
    end

validate_format(errors = nil) click to toggle source

Format validation.

If an array is given as the argument, when errors are found, error objects are pushed to the array. Currently, following errors may be added to the array. (All errors are under the Bio::Fastq namespace, for example, Bio::Fastq::Error::Diff_ids).

Error::Diff_ids -- the identifier in the two lines are different Error::Long_qual -- length of quality is longer than the sequence Error::Short_qual -- length of quality is shorter than the sequence Error::No_qual -- no quality characters found Error::No_seq -- no sequence found Error::Qual_char -- invalid character in the quality Error::Seq_char -- invalid character in the sequence Error::Qual_range -- quality score value out of range Error::No_ids -- sequence identifier not found Error::No_atmark -- the first identifier does not begin with "@" Error::Skipped_unformatted_lines -- the parser skipped unformatted lines that could not be recognized as FASTQ format

Arguments:

- (optional) errors: (Array or nil) an array for pushing error messages. The array should be empty.

Returns | true:no error, false: containing error.

    # File lib/bio/db/fastq.rb, line 562
    def validate_format(errors = nil)
      err = []

      # if header exists, the format might be broken.
      if defined? @header and @header and !@header.strip.empty? then
        err.push Error::Skipped_unformatted_lines.new
      end

      # if parse errors exist, adding them
      if defined? @parse_errors and @parse_errors then
        err.concat @parse_errors
      end

      # check if identifier exists, and identifier matches
      if !defined?(@definition) or !@definition then
        err.push Error::No_ids.new
      elsif defined?(@definition2) and
          !@definition2.to_s.empty? and
          @definition != @definition2 then
        err.push Error::Diff_ids.new
      end

      # check if sequence exists
      has_seq  = true
      if !defined?(@sequence_string) or !@sequence_string then
        err.push Error::No_seq.new
        has_seq = false
      end

      # check if quality exists
      has_qual = true
      if !defined?(@quality_string) or !@quality_string then
        err.push Error::No_qual.new
        has_qual = false
      end

      # sequence and quality length check
      if has_seq and has_qual then
        slen = @sequence_string.length
        qlen = @quality_string.length
        if slen > qlen then
          err.push Error::Short_qual.new
        elsif qlen > slen then
          err.push Error::Long_qual.new
        end
      end

      # sequence character check
      if has_seq then
        sc = StringScanner.new(@sequence_string)
        while sc.scan_until(/[ \x00-\x1f\x7f-\xff]/)
          err.push Error::Seq_char.new(sc.pos - sc.matched_size)
        end
      end

      # sequence character check
      if has_qual then
        fmt = if defined?(@format) and @format then
                @format.name
              else
                nil
              end
        re = case fmt
             when 'fastq-sanger'
               /[^\x21-\x7e]/
             when 'fastq-solexa'
               /[^\x3b-\x7e]/
             when 'fastq-illumina'
               /[^\x40-\x7e]/
             else
               /[ \x00-\x1f\x7f-\xff]/
             end
        sc = StringScanner.new(@quality_string)
        while sc.scan_until(re)
          err.push Error::Qual_char.new(sc.pos - sc.matched_size)
        end
      end

      # if "errors" is given, set errors
      errors.concat err if errors
      # returns true if no error; otherwise, returns false
      err.empty? ? true : false
    end

[Validate]

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