### Home Classes Methods

### In Files

- lib/bio/db/rebase.rb

### Parent

Object

### Methods

- ::load_yaml
- ::new
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- #each
- #enzyme_name?
- #enzymes
- #parse_enzymes
- #parse_references
- #parse_suppliers
- #raw_to_reference
- #save_yaml
- #setup_enzyme_and_reference_association
- #setup_enzyme_data

### 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
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- Bio::Alignment::FactoryTemplate::FileInFileOut
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- Bio::EMBL
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- Bio::Ensembl
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- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
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- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
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- Bio::Fasta::Report::Program
- Bio::FastaDefline
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- Bio::Fastq
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- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
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- Bio::Feature
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- Bio::Features
- Bio::Fetch
- Bio::FlatFile
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- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
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- 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
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- 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
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- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
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- Bio::MAFFT::Report
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- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
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- 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
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
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- Bio::PROSITE
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- Bio::PSORT::CGIDriver
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- Bio::PSORT::PSORT1
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- Bio::PTS1
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- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::PhyloXML
- Bio::PhyloXML::Accession
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- Bio::PhyloXML::BranchColor
- Bio::PhyloXML::CladeRelation
- Bio::PhyloXML::Confidence
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- 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
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- 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
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- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
- Bio::SQL::BioentryRelationship
- Bio::SQL::Biosequence
- Bio::SQL::Comment
- Bio::SQL::Dbxref
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- 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
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- 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
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- Bio::Sequence::Format::FormatterBase
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- Bio::Sequence::QualityScore::Converter
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- Bio::Sequence::SequenceMasker
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- Bio::SiRNA
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- Bio::Spidey
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- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
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- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
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- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
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- 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::REBASE

bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files

Author | Trevor Wennblom <trevor@corevx.com>
Copyright | Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com)
License | The Ruby License

# Description

Bio::REBASE provides utilties for interacting with REBASE data in EMBOSS format. REBASE is the Restriction Enzyme Database, more information can be found here:

- rebase.neb.com

EMBOSS formatted files located at:

- rebase.neb.com/rebase/rebase.f37.html

These files are the same as the "emboss_?.???" files located at:

- ftp.neb.com/pub/rebase/

To easily get started with the data you can simply type this command at your shell prompt:

    % wget "ftp://ftp.neb.com/pub/rebase/emboss_*"

# Usage

    require 'bio'
    require 'pp'

    enz = File.read('emboss_e')
    ref = File.read('emboss_r')
    sup = File.read('emboss_s')

    # When creating a new instance of Bio::REBASE
    # the contents of the enzyme file must be passed.
    # The references and suppiers file contents
    # may also be passed.
    rebase = Bio::REBASE.new( enz )
    rebase = Bio::REBASE.new( enz, ref )
    rebase = Bio::REBASE.new( enz, ref, sup )

    # The 'read' class method allows you to read in files
    # that are REBASE EMBOSS formatted
    rebase = Bio::REBASE.read( 'emboss_e' )
    rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
    rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )

    # The data loaded may be saved in YAML format
    rebase.save_yaml( 'enz.yaml' )
    rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
    rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )

    # YAML formatted files can also be read with the
    # class method 'load_yaml'
    rebase = Bio::REBASE.load_yaml( 'enz.yaml' )
    rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
    rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )

    pp rebase.enzymes[0..4]                     # ["AarI", "AasI", "AatI", "AatII", "Acc16I"]
    pp rebase.enzyme_name?('aasi')              # true
    pp rebase['AarI'].pattern                   # "CACCTGC"
    pp rebase['AarI'].blunt?                    # false
    pp rebase['AarI'].organism                  # "Arthrobacter aurescens SS2-322"
    pp rebase['AarI'].source                    # "A. Janulaitis"
    pp rebase['AarI'].primary_strand_cut1       # 11
    pp rebase['AarI'].primary_strand_cut2       # 0
    pp rebase['AarI'].complementary_strand_cut1 # 15
    pp rebase['AarI'].complementary_strand_cut2 # 0
    pp rebase['AarI'].suppliers                 # ["F"]
    pp rebase['AarI'].supplier_names            # ["Fermentas International Inc."]

    pp rebase['AarI'].isoschizomers             # Currently none stored in the references file
    pp rebase['AarI'].methylation               # ""

    pp rebase['EcoRII'].methylation             # "2(5)"
    pp rebase['EcoRII'].suppliers               # ["F", "J", "M", "O", "S"]
    pp rebase['EcoRII'].supplier_names  # ["Fermentas International Inc.", "Nippon Gene Co., Ltd.",
                                        # "Roche Applied Science", "Toyobo Biochemicals",
                                        # "Sigma Chemical Corporation"]

    # Number of enzymes in the database
    pp rebase.size                              # 673
    pp rebase.enzymes.size                      # 673

    rebase.each do |name, info|
      pp "#{name}:  #{info.methylation}" unless info.methylation.empty?
    end

### Public Class Methods

load_yaml( f_enzyme, f_reference=nil, f_supplier=nil ) click to toggle source

Read YAML formatted files

    rebase = Bio::REBASE.load_yaml( 'enz.yaml' )
    rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
    rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )

Arguments

- `f_enzyme`: (required) Filename to read YAML-formatted enzyme data

- `f_reference`: (optional) Filename to read YAML-formatted reference data

- `f_supplier`: (optional) Filename to read YAML-formatted supplier data

Returns | Bio::REBASE object

    # File lib/bio/db/rebase.rb, line 258
    def self.load_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
      e = YAML.load_file(f_enzyme)
      r = f_reference ? YAML.load_file(f_reference) : nil
      s = f_supplier ? YAML.load_file(f_supplier) : nil
      self.new(e,r,s,true)
    end

new( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false ) click to toggle source

Constructor

Arguments

- `enzyme_lines`: (required) contents of EMBOSS formatted enzymes file

- `reference_lines`: (optional) contents of EMBOSS formatted references file

- `supplier_lines`: (optional) contents of EMBOSS formatted suppliers files

- `yaml`: (optional, default `false`) enzyme_lines, reference_lines, and supplier_lines are read as YAML if set to true

Returns | Bio::REBASE

    # File lib/bio/db/rebase.rb, line 174
    def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false )
      # All your REBASE are belong to us.

      if yaml
        @enzyme_data = enzyme_lines
        @reference_data = reference_lines
        @supplier_data = supplier_lines
      else
        @enzyme_data = parse_enzymes(enzyme_lines)
        @reference_data = parse_references(reference_lines)
        @supplier_data = parse_suppliers(supplier_lines)
      end

      EnzymeEntry.supplier_data = @supplier_data
      setup_enzyme_data
    end

read( f_enzyme, f_reference=nil, f_supplier=nil ) click to toggle source

Read REBASE EMBOSS-formatted files

    rebase = Bio::REBASE.read( 'emboss_e' )
    rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
    rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )

Arguments

- `f_enzyme`: (required) Filename to read enzyme data

- `f_reference`: (optional) Filename to read reference data

- `f_supplier`: (optional) Filename to read supplier data

Returns | Bio::REBASE object

    # File lib/bio/db/rebase.rb, line 240
    def self.read( f_enzyme, f_reference=nil, f_supplier=nil )
      e = IO.readlines(f_enzyme)
      r = f_reference ? IO.readlines(f_reference) : nil
      s = f_supplier ? IO.readlines(f_supplier) : nil
      self.new(e,r,s)
    end

### Public Instance Methods

each() click to toggle source

Calls block once for each element in `@data` hash, passing that element as a parameter.

Arguments

- Accepts a block

Returns | results of block operations

    # File lib/bio/db/rebase.rb, line 150
    def each
      @data.each { |item| yield item }
    end

enzyme_name?(name) click to toggle source

Check if supplied name is the name of an available enzyme

Arguments

- `name`: Enzyme name

Returns | `true/false`

    # File lib/bio/db/rebase.rb, line 207
    def enzyme_name?(name)
      @enzyme_names_downcased.include?(name.downcase)
    end

enzymes() click to toggle source

List the enzymes available

Arguments

- none

Returns | `Array` sorted enzyme names

    # File lib/bio/db/rebase.rb, line 197
    def enzymes
      @enzyme_names
    end

save_yaml( f_enzyme, f_reference=nil, f_supplier=nil ) click to toggle source

Save the current data

    rebase.save_yaml( 'enz.yaml' )
    rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
    rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )

Arguments

- `f_enzyme`: (required) Filename to save YAML formatted output of enzyme data

- `f_reference`: (optional) Filename to save YAML formatted output of reference data

- `f_supplier`: (optional) Filename to save YAML formatted output of supplier data

Returns | nothing

    # File lib/bio/db/rebase.rb, line 222
    def save_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
      File.open(f_enzyme, 'w') { |f| f.puts YAML.dump(@enzyme_data) }
      File.open(f_reference, 'w') { |f| f.puts YAML.dump(@reference_data) } if f_reference
      File.open(f_supplier, 'w') { |f| f.puts YAML.dump(@supplier_data) } if f_supplier
      return
    end

### Protected Instance Methods

parse_enzymes( lines ) click to toggle source

data is a hash indexed by the :name of each entry which is also a hash

- data has the following keys: :name, :pattern, :len, :ncuts, :blunt, :c1, :c2, :c3, :c4 :c1 => First 5' cut :c2 => First 3' cut :c3 => Second 5' cut :c4 => Seocnd 3' cut

    # File lib/bio/db/rebase.rb, line 314
    def parse_enzymes( lines )
      data = {}
      return data if lines == nil
      lines.each_line do |line|
        next if line[0].chr == '#'
        line.chomp!

        a = line.split("\s")

        data[ a[0] ] = {
          :name => a[0],
          :pattern => a[1],
          :len => a[2],
          :ncuts => a[3],
          :blunt => a[4],
          :c1 => a[5],
          :c2 => a[6],
          :c3 => a[7],
          :c4 => a[8]
        }
      end  # lines.each
      data
    end

parse_references( lines ) click to toggle source

data is a hash indexed by the :name of each entry which is also a hash

- data has the following keys: :organism, :isoschizomers, :references, :source, :methylation, :suppliers, :name, :number_of_references

    # File lib/bio/db/rebase.rb, line 341
    def parse_references( lines )
      data = {}
      return data if lines == nil
      index = 1
      h = {}
      references_left = 0

      lines.each_line do |line|
        next if line[0].chr == '#'  # Comment
        next if line[0..1] == '//'  # End of entry marker
        line.chomp!

        if (1..7).include?( index )
          h[index] = line
          references_left = h[index].to_i if index == 7
          index += 1
          next
        end

        if index == 8
          h[index] ||= []
          h[index] << line
          references_left -= 1
        end

        if references_left == 0
          data[ h[1] ] = {
            :name => h[1],
            :organism => h[2],
            :isoschizomers => h[3],
            :methylation => h[4],
            :source => h[5],
            :suppliers => h[6],
            :number_of_references => h[7],
            :references => h[8]
          }
          index = 1
          h = {}
        end
      end  # lines.each
      data
    end

parse_suppliers( lines ) click to toggle source

data is a hash indexed by the supplier code

    data[supplier_code]
    returns the suppliers name

    # File lib/bio/db/rebase.rb, line 387
    def parse_suppliers( lines )
      data = {}
      return data if lines == nil
      lines.each_line do |line|
        next if line[0].chr == '#'
        data[$1] = $2 if line =~ %{(.+?)\s(.+)}
      end
      data
    end

raw_to_reference( line ) click to toggle source

Takes a string in one of the three formats listed below and returns a Bio::Reference object

- Possible input styles: a = 'Inagaki, K., Hikita, T., Yanagidani, S., Nomura, Y., Kishimoto, N., Tano, T., Tanaka, H., (1993) Biosci. Biotechnol. Biochem., vol. 57, pp. 1716-1721.' b = 'Nekrasiene, D., Lapcinskaja, S., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.' c = "Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30."

    # File lib/bio/db/rebase.rb, line 403
    def raw_to_reference( line )
      a = line.split(', ')

      if a[-1] == 'Unpublished observations.'
        title = a.pop.chop
        pages = volume = year = journal = ''
      else
        title = ''

        pages_or_volume = a.pop.chop
        if pages_or_volume =~ %{pp\.\s}
          pages = pages_or_volume
          pages.gsub!('pp. ', '')
          volume = a.pop
        else
          pages = ''
          volume = pages_or_volume
        end

        volume.gsub!('vol. ', '')

        year_and_journal = a.pop
        year_and_journal =~ %{\((\d+)\)\s(.+)}
        year = $1
        journal = $2
      end

      authors = []

      last_name = nil
      a.each do |e|
        if last_name
          authors << "#{last_name}, #{e}"
          last_name = nil
        else
          last_name = e
        end
      end

      ref = {
        'title' => title,
        'pages' => pages,
        'volume' => volume,
        'year' => year,
        'journal' => journal,
        'authors' => authors,
      }

      Bio::Reference.new(ref)
    end

setup_enzyme_and_reference_association() click to toggle source

    # File lib/bio/db/rebase.rb, line 295
    def setup_enzyme_and_reference_association
      return unless @reference_data
      @reference_data.each do |name, hash|
        d = @data[name]
        [:organism, :isoschizomers,
        :methylation, :source].each { |k| d[k] = hash[k] }
        d.suppliers = hash[:suppliers].split('')
        d.references = []
        hash[:references].each { |k| d.references << raw_to_reference(k) }
      end
    end

setup_enzyme_data() click to toggle source

    # File lib/bio/db/rebase.rb, line 269
    def setup_enzyme_data
      @data = {}

      @enzyme_data.each do |name, hash|
        @data[name] = EnzymeEntry.new
        d = @data[name]
        d.pattern                   = hash[:pattern]
        # d.blunt?= is a syntax error
        d[:blunt?] = (hash[:blunt].to_i == 1 ? true : false)
        d.primary_strand_cut1       = hash[:c1].to_i
        d.complementary_strand_cut1 = hash[:c2].to_i
        d.primary_strand_cut2       = hash[:c3].to_i
        d.complementary_strand_cut2 = hash[:c4].to_i

        # Set up keys just in case there's no reference data supplied
        [:organism, :isoschizomers,
        :methylation, :source].each { |k| d[k] = '' }
        d.suppliers = []
        d.references = []
      end

      @enzyme_names = @data.keys.sort
      @enzyme_names_downcased = @enzyme_names.map{|a| a.downcase}
      setup_enzyme_and_reference_association
    end

[Validate]

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