### Home Classes Methods

### In Files

- lib/bio/io/fastacmd.rb
- lib/bio/appl/bl2seq/report.rb
- lib/bio/appl/blast/format8.rb
- lib/bio/appl/blast/remote.rb
- lib/bio/appl/blast/xmlparser.rb
- lib/bio/appl/blast/rpsblast.rb
- lib/bio/appl/blast/wublast.rb
- lib/bio/appl/blast/report.rb
- lib/bio/appl/blast/ncbioptions.rb
- lib/bio/appl/blast/rexml.rb
- lib/bio/appl/blast/format0.rb
- lib/bio/appl/blast.rb

### Parent

Object

### Namespace

- MODULE Bio::Blast::Default
- MODULE Bio::Blast::RPSBlast
- MODULE Bio::Blast::Remote
- MODULE Bio::Blast::WU
- CLASS Bio::Blast::Bl2seq
- CLASS Bio::Blast::Fastacmd
- CLASS Bio::Blast::NCBIOptions
- CLASS Bio::Blast::Report
- CLASS Bio::Blast::Report_tab

### Methods

- ::local
- ::new
- ::remote
- ::reports
- ::reports_xml
- #option
- #option=
- #options=
- #query
- #server=

### Files

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

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
- Bio::Alignment
- Bio::Alignment::ArrayExtension
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- 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::FLATFILE_SPLITTER
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
- Bio::DAS::TARGET
- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DBGET
- Bio::DDBJ
- Bio::DDBJ::REST
- Bio::DDBJ::REST::Blast
- Bio::DDBJ::REST::ClustalW
- Bio::DDBJ::REST::DDBJ
- Bio::DDBJ::REST::Mafft
- Bio::DDBJ::REST::RequestManager
- Bio::DDBJ::REST::WABItemplate
- Bio::DDBJ::XML
- Bio::DDBJ::XML::Blast
- Bio::DDBJ::XML::ClustalW
- Bio::DDBJ::XML::DDBJ
- Bio::DDBJ::XML::Fasta
- Bio::DDBJ::XML::GetEntry
- Bio::DDBJ::XML::Gib
- Bio::DDBJ::XML::Gtop
- Bio::DDBJ::XML::PML
- Bio::DDBJ::XML::RequestManager
- Bio::DDBJ::XML::RequestManager::REST
- Bio::DDBJ::XML::SRS
- Bio::DDBJ::XML::TxSearch
- Bio::EBI
- Bio::EBI::SOAP
- Bio::EBI::SOAP::Citation
- Bio::EBI::SOAP::ClustalW
- Bio::EBI::SOAP::Dbfetch
- Bio::EBI::SOAP::Emboss
- Bio::EBI::SOAP::Fasta
- Bio::EBI::SOAP::InterProScan
- Bio::EBI::SOAP::MPsrch
- Bio::EBI::SOAP::MSD
- Bio::EBI::SOAP::Muscle
- Bio::EBI::SOAP::Ontology
- Bio::EBI::SOAP::ScanPS
- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FLATFILE_SPLITTER
- 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::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::Edge
- Bio::Newick::Node
- 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::Blast

## Description

The Bio::Blast class contains methods for running local or remote BLAST searches, as well as for parsing of the output of such BLASTs (i.e. the BLAST reports). For more information on similarity searches and the BLAST program, see www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html.

## Usage

    require 'bio'

    # To run an actual BLAST analysis:
    #   1. create a BLAST factory
    remote_blast_factory = Bio::Blast.remote('blastp', 'swissprot',
                                             '-e 0.0001', 'genomenet')
    #or:
    local_blast_factory = Bio::Blast.local('blastn','/path/to/db')

    #   2. run the actual BLAST by querying the factory
    report = remote_blast_factory.query(sequence_text)

    # Then, to parse the report, see Bio::Blast::Report

## See also

- Bio::Blast::Report

- Bio::Blast::Report::Hit

- Bio::Blast::Report::Hsp

## References

- www.ncbi.nlm.nih.gov/blast/

- www.ncbi.nlm.nih.gov/Education/BLASTinfo/similarity.html

- blast.genome.jp/ideas/ideas.html#blast

### Attributes

blastall[RW]

Full path for blastall. (default: 'blastall').

db[RW]

Database name (-d option for blastall)

filter[RW]

Filter option for blastall -F (T or F).

format[RW]

Output report format for blastall -m

0, pairwise; 1; 2; 3; 4; 5; 6; 7, XML Blast outpu;, 8, tabular; 9, tabular with comment lines; 10, ASN text; 11, ASN binery [intege].

matrix[RW]

Substitution matrix for blastall -M

options[R]

Options for blastall

output[R]

Returns a String containing blast execution output in as is the Bio::Blast#format.

parser[W]
program[RW]

Program name (-p option for blastall): blastp, blastn, blastx, tblastn or tblastx

server[R]

Server to submit the BLASTs to

### Public Class Methods

local(program, db, options = '', blastall = nil) click to toggle source

This is a shortcut for Bio::Blast.new:

    Bio::Blast.local(program, database, options)

is equivalent to

    Bio::Blast.new(program, database, options, 'local')

Arguments:

- program (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'

- db (required): name of the local database

- options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

- blastall: full path to blastall program (e.g. "/opt/bin/blastall"; DEFAULT: "blastall")

Returns | Bio::Blast factory object

    # File lib/bio/appl/blast.rb, line 79
    def self.local(program, db, options = '', blastall = nil)
      f = self.new(program, db, options, 'local')
      if blastall then
        f.blastall = blastall
      end
      f
    end

new(program, db, opt = [], server = 'local') click to toggle source

Creates a Bio::Blast factory object.

To run any BLAST searches, a factory has to be created that describes a certain BLAST pipeline: the program to use, the database to search, any options and the server to use. E.g.

    blast_factory = Bio::Blast.new('blastn','dbsts', '-e 0.0001 -r 4', 'genomenet')

Arguments:

- program (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'

- db (required): name of the (local or remote) database

- options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

- server: server to use (e.g. 'genomenet'; DEFAULT = 'local')

Returns | Bio::Blast factory object

    # File lib/bio/appl/blast.rb, line 317
    def initialize(program, db, opt = [], server = 'local')
      @program  = program
      @db       = db

      @blastall = 'blastall'
      @matrix   = nil
      @filter   = nil

      @output   = ''
      @parser   = nil
      @format   = nil

      @options = set_options(opt, program, db)
      self.server = server
    end

remote(program, db, option = '', server = 'genomenet') click to toggle source

Bio::Blast.remote does exactly the same as Bio::Blast.new, but sets the remote server 'genomenet' as its default.

Arguments:

- program (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'

- db (required): name of the remote database

- options: blastall options \

(see www.genome.jp/dbget-bin/show_man?blast2)

- server: server to use (DEFAULT = 'genomenet')

Returns | Bio::Blast factory object

    # File lib/bio/appl/blast.rb, line 97
    def self.remote(program, db, option = '', server = 'genomenet')
      self.new(program, db, option, server)
    end

reports(input, parser = nil) click to toggle source

Bio::Blast.report parses given data, and returns an array of report (Bio::Blast::Report or Bio::Blast::Default::Report) objects, or yields each report object when a block is given.

Supported formats: NCBI default (-m 0), XML (-m 7), tabular (-m 8).

Arguments:

- input (required): input data

- parser: type of parser. see Bio::Blast::Report.new

Returns | Undefiend when a block is given. Otherwise, an Array containing report (Bio::Blast::Report or Bio::Blast::Default::Report) objects.

    # File lib/bio/appl/blast.rb, line 114
    def self.reports(input, parser = nil)
      begin
        istr = input.to_str
      rescue NoMethodError
        istr = nil
      end
      if istr then
        input = StringIO.new(istr)
      end
      raise 'unsupported input data type' unless input.respond_to?(:gets)

      # if proper parser is given, emulates old behavior.
      case parser
      when :xmlparser, :rexml
        ff = Bio::FlatFile.new(Bio::Blast::Report, input)
        if block_given? then
          ff.each do |e|
            yield e
          end
          return []
        else
          return ff.to_a
        end
      when :tab
        istr = input.read unless istr
        rep = Report.new(istr, parser)
        if block_given? then
          yield rep
          return []
        else
          return [ rep ]
        end
      end

      # preparation of the new format autodetection rule if needed
      if !defined?(@@reports_format_autodetection_rule) or
          !@@reports_format_autodetection_rule then
        regrule = Bio::FlatFile::AutoDetect::RuleRegexp
        blastxml = regrule[ 'Bio::Blast::Report',
                            /\<\!DOCTYPE BlastOutput PUBLIC / ]
        blast    = regrule[ 'Bio::Blast::Default::Report',
                            /^BLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ]
        tblast   = regrule[ 'Bio::Blast::Default::Report_TBlast',
                            /^TBLAST.? +[\-\.\w]+ +\[[\-\.\w ]+\]/ ]
        tab      = regrule[ 'Bio::Blast::Report_tab',
                            /^([^\t]*\t){11}[^\t]*$/ ]
        auto = Bio::FlatFile::AutoDetect[ blastxml,
                                          blast,
                                          tblast,
                                          tab
                                        ]
        # sets priorities
        blastxml.is_prior_to blast
        blast.is_prior_to tblast
        tblast.is_prior_to tab
        # rehash
        auto.rehash
        @@report_format_autodetection_rule = auto
      end

      # Creates a FlatFile object with dummy class
      ff = Bio::FlatFile.new(Object, input)
      ff.dbclass = nil

      # file format autodetection
      3.times do
        break if ff.eof? or
          ff.autodetect(31, @@report_format_autodetection_rule)
      end
      # If format detection failed, assumed to be tabular (-m 8)
      ff.dbclass = Bio::Blast::Report_tab unless ff.dbclass

      if block_given? then
        ff.each do |entry|
          yield entry
        end
        ret = []
      else
        ret = ff.to_a
      end
      ret
    end

reports_xml(input, parser = nil) click to toggle source

Note that this is the old implementation of Bio::Blast.reports. The aim of this method is keeping compatibility for older BLAST XML documents which might not be parsed by the new Bio::Blast.reports nor Bio::FlatFile. (Though we are not sure whether such documents exist or not.)

Bio::Blast.reports_xml parses given data, and returns an array of Bio::Blast::Report objects, or yields each Bio::Blast::Report object when a block is given.

It can be used only for XML format. For default (-m 0) format, consider using Bio::FlatFile, or Bio::Blast.reports.

Arguments:

- input (required): input data

- parser: type of parser. see Bio::Blast::Report.new

Returns | Undefiend when a block is given. Otherwise, an Array containing Bio::Blast::Report objects.

    # File lib/bio/appl/blast.rb, line 220
    def self.reports_xml(input, parser = nil)
      ary = []
      input.each_line("</BlastOutput>\n") do |xml|
        xml.sub!(/[^<]*(<?)/, '\1') # skip before <?xml> tag
        next if xml.empty?          # skip trailing no hits
        rep = Report.new(xml, parser)
        if rep.reports then
          if block_given?
            rep.reports.each { |r| yield r }
          else
            ary.concat rep.reports
          end
        else
          if block_given?
            yield rep
          else
            ary.push rep
          end
        end
      end
      return ary
    end

### Public Instance Methods

option() click to toggle source

Returns options of blastall

    # File lib/bio/appl/blast.rb, line 374
    def option
      # backward compatibility
      Bio::Command.make_command_line(options)
    end

option=(str) click to toggle source

Set options for blastall

    # File lib/bio/appl/blast.rb, line 380
    def option=(str)
      # backward compatibility
      self.options = Shellwords.shellwords(str)
    end

options=(ary) click to toggle source

Sets options for blastall

    # File lib/bio/appl/blast.rb, line 255
    def options=(ary)
      @options = set_options(ary)
    end

query(query) click to toggle source

This method submits a sequence to a BLAST factory, which performs the actual BLAST.

    # example 1
    seq = Bio::Sequence::NA.new('agggcattgccccggaagatcaagtcgtgctcctg')
    report = blast_factory.query(seq)

    # example 2
    str <<END_OF_FASTA
    >lcl|MySequence
    MPPSAISKISNSTTPQVQSSSAPNLTMLEGKGISVEKSFRVYSEEENQNQHKAKDSLGF
    KELEKDAIKNSKQDKKDHKNWLETLYDQAEQKWLQEPKKKLQDLIKNSGDNSRVILKDS
    END_OF_FASTA
    report = blast_factory.query(str)

Bug note: When multi-FASTA is given and the format is 7 (XML) or 8 (tab), it should return an array of Bio::Blast::Report objects, but it returns a single Bio::Blast::Report object. This is a known bug and should be fixed in the future.

Arguments:

- query (required): single- or multiple-FASTA formatted sequence(s)

Returns | a Bio::Blast::Report (or Bio::Blast::Default::Report) object when single query is given. When multiple sequences are given as the query, it returns an array of Bio::Blast::Report (or Bio::Blast::Default::Report) objects. If it can not parse result, nil will be returnd.

    # File lib/bio/appl/blast.rb, line 358
    def query(query)
      case query
      when Bio::Sequence
        query = query.output(:fasta)
      when Bio::Sequence::NA, Bio::Sequence::AA, Bio::Sequence::Generic
        query = query.to_fasta('query', 70)
      else
        query = query.to_s
      end

      @output = self.__send__("exec_#{@server}", query)
      report = parse_result(@output)
      return report
    end

server=(str) click to toggle source

Sets server to submit the BLASTs to. The exec_xxxx method should be defined in Bio::Blast or Bio::Blast::Remote::Xxxx class.

    # File lib/bio/appl/blast.rb, line 265
    def server=(str)
      @server = str
      begin
        m = Bio::Blast::Remote.const_get(@server.capitalize)
      rescue NameError
        m = nil
      end
      if m and !(self.is_a?(m)) then
        # lazy include Bio::Blast::Remote::XXX module
        self.class.class_eval { include m }
      end
      return @server
    end

[Validate]

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