### Home Classes Methods

### In Files

- lib/bio/db/kegg/genes.rb

### Parent

Bio::KEGGDB

### Methods

- ::new
- #aalen
- #aaseq
- #chromosome
- #codon_usage
- #cu_list
- #dblinks
- #dblinks_as_hash
- #dblinks_as_strings
- #definition
- #division
- #eclinks
- #entry
- #entry_id
- #gbposition
- #gene
- #genes
- #keggclass
- #keggclasses
- #locations
- #motif
- #motifs
- #motifs_as_hash
- #motifs_as_strings
- #nalen
- #name
- #names
- #names_as_array
- #naseq
- #ntlen
- #ntseq
- #organism
- #orthologs
- #orthologs_as_hash
- #orthologs_as_strings
- #pathway
- #pathways
- #pathways_as_hash
- #pathways_as_strings
- #position
- #structure
- #structures

### Included Modules

- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::OrthologsAsHash

### 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
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- Bio::FlatFile::AutoDetect::RuleRegexp
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- Bio::FlatFileIndex::BDB_1
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- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
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- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
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- Bio::FlatFileIndex::NameSpaces
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- Bio::GCG
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- Bio::GO
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- Bio::GenBank
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- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
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- Bio::Hinv
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- Bio::Iprscan
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- Bio::KEGG
- Bio::KEGG::API
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- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
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- Bio::KEGG::Common::References
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- Bio::KEGG::DRUG
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- Bio::KEGG::EXPRESSION
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- Bio::PhyloXML::SequenceRelation
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- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
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- Bio::Sequence::Format::AminoFormatter
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- Bio::UniProt
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- Hash
- Object
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No matching classes.

# Bio::KEGG::GENES

## Description

KEGG GENES entry parser.

## References

- www.genome.jp/kegg/genes.html

### Constants

DELIMITER
TAGSIZE

### Public Class Methods

new(entry) click to toggle source

Creates a new Bio::KEGG::GENES object.

Arguments:

- (required) entry: (String) single entry as a string

Returns | Bio::KEGG::GENES object

    # File lib/bio/db/kegg/genes.rb, line 115
    def initialize(entry)
      super(entry, TAGSIZE)
    end

### Public Instance Methods

aalen() click to toggle source

Returns length of the amino acid sequence described in the AASEQ lines.

Returns | Integer

    # File lib/bio/db/kegg/genes.rb, line 393
    def aalen
      fetch('AASEQ')[/\d+/].to_i
    end

aaseq() click to toggle source

Returns amino acid sequence described in the AASEQ lines.

Returns | Bio::Sequence::AA object

    # File lib/bio/db/kegg/genes.rb, line 383
    def aaseq
      unless @data['AASEQ']
        @data['AASEQ'] = Bio::Sequence::AA.new(fetch('AASEQ').gsub(/\d+/, ''))
      end
      @data['AASEQ']
    end

chromosome() click to toggle source

Chromosome described in the POSITION line.

Returns | String or nil

    # File lib/bio/db/kegg/genes.rb, line 264
    def chromosome
      if position[/:/]
        position.sub(/:.*/, '')
      elsif ! position[/\.\./]
        position
      else
        nil
      end
    end

codon_usage(codon = nil) click to toggle source

Codon usage data described in the CODON_USAGE lines. (Deprecated: no more exists)

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 350
    def codon_usage(codon = nil)
      unless @data['CODON_USAGE']
        hash = Hash.new
        list = cu_list
        base = %(t c a g)
        base.each_with_index do |x, i|
          base.each_with_index do |y, j|
            base.each_with_index do |z, k|
              hash["#{x}#{y}#{z}"] = list[i*16 + j*4 + k]
            end
          end
        end
        @data['CODON_USAGE'] = hash
      end
      @data['CODON_USAGE']
    end

cu_list() click to toggle source

Codon usage data described in the CODON_USAGE lines as an array.

Returns | Array

    # File lib/bio/db/kegg/genes.rb, line 370
    def cu_list
      ary = []
      get('CODON_USAGE').sub(/.*/,'').each_line do |line| # cut 1st line
        line.chomp.sub(/^.{11}/, '').scan(/..../) do |cu|
          ary.push(cu.to_i)
        end
      end
      return ary
    end

dblinks() click to toggle source
Alias for: dblinks_as_hash
dblinks_as_hash() click to toggle source

Returns a Hash of the DB name and an Array of entry IDs in DBLINKS field.

    # File lib/bio/db/kegg/genes.rb, line 97
    def dblinks_as_hash; super; end

Also aliased as: dblinks
dblinks_as_strings() click to toggle source

Links to other databases described in the DBLINKS lines.

Returns | Array containing String objects

    # File lib/bio/db/kegg/genes.rb, line 332
    def dblinks_as_strings
      lines_fetch('DBLINKS')
    end

definition() click to toggle source

Definition of the entry, described in the DEFINITION line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 199
    def definition
      field_fetch('DEFINITION')
    end

division() click to toggle source

Division of the entry, described in the ENTRY line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 149
    def division
      entry['division']                   # CDS, tRNA etc.
    end

eclinks() click to toggle source

Enzyme's EC numbers shown in the DEFINITION line.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 206
    def eclinks
      unless defined? @eclinks
        ec_list =
          definition.slice(/\[EC\:([^\]]+)\]/, 1) ||
          definition.slice(/\(EC\:([^\)]+)\)/, 1)
        ary = ec_list ? ec_list.strip.split(/\s+/) : []
        @eclinks = ary
      end
      @eclinks
    end

entry() click to toggle source

Returns the "ENTRY" line content as a Hash. For example,

    {"organism"=>"E.coli", "division"=>"CDS", "id"=>"b0356"}

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 125
    def entry
      unless @data['ENTRY']
        hash = Hash.new('')
        if get('ENTRY').length > 30
          e = get('ENTRY')
          hash['id']       = e[12..29].strip
          hash['division'] = e[30..39].strip
          hash['organism'] = e[40..80].strip
        end
        @data['ENTRY'] = hash
      end
      @data['ENTRY']
    end

entry_id() click to toggle source

ID of the entry, described in the ENTRY line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 142
    def entry_id
      entry['id']
    end

gbposition() click to toggle source

The position in the genome described in the POSITION line as GenBank feature table location formatted string.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 278
    def gbposition
      position.sub(/.*?:/, '')
    end

gene() click to toggle source

The method will be deprecated. Use `entry.names.first` instead.

Returns the first gene name described in the NAME line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 192
    def gene
      genes.first
    end

genes() click to toggle source

The method will be deprecated. Use Bio::KEGG::GENES#names.

Names of the entry as an Array, described in the NAME line.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 182
    def genes
      names_as_array
    end

keggclass() click to toggle source

Returns CLASS field of the entry.

    # File lib/bio/db/kegg/genes.rb, line 242
    def keggclass
      field_fetch('CLASS')
    end

keggclasses() click to toggle source

Returns an Array of biological classes in CLASS field.

    # File lib/bio/db/kegg/genes.rb, line 247
    def keggclasses
      keggclass.gsub(/ \[[^\]]+/, '').split(/\] ?/)
    end

locations() click to toggle source

The position in the genome described in the POSITION line as Bio::Locations object.

Returns | Bio::Locations object

    # File lib/bio/db/kegg/genes.rb, line 286
    def locations
      Bio::Locations.new(gbposition)
    end

motif() click to toggle source

The specification of the method will be changed in the future. Please use Bio::KEGG::GENES#motifs.

Motif information described in the MOTIF lines.

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 325
    def motif
      motifs
    end

motifs() click to toggle source
Alias for: motifs_as_hash
motifs_as_hash() click to toggle source

Motif information described in the MOTIF lines.

Returns | Hash

    # File lib/bio/db/kegg/genes.rb, line 300
    def motifs_as_hash
      unless @data['MOTIF']
        hash = {}
        db = nil
        motifs_as_strings.each do |line|
          if line[/^\S+:/]
            db, str = line.split(/:/, 2)
          else
            str = line
          end
          hash[db] ||= []
          hash[db] += str.strip.split(/\s+/)
        end
        @data['MOTIF'] = hash
      end
      @data['MOTIF']              # Hash of Array of IDs in MOTIF
    end

Also aliased as: motifs
motifs_as_strings() click to toggle source

Motif information described in the MOTIF lines.

Returns | Strings

    # File lib/bio/db/kegg/genes.rb, line 293
    def motifs_as_strings
      lines_fetch('MOTIF')
    end

nalen() click to toggle source
Alias for: ntlen
name() click to toggle source

Returns the NAME line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 163
    def name
      field_fetch('NAME')
    end

names() click to toggle source
Alias for: names_as_array
names_as_array() click to toggle source

Names of the entry as an Array, described in the NAME line.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 171
    def names_as_array
      name.split(', ')
    end

Also aliased as: names
naseq() click to toggle source
Alias for: ntseq
ntlen() click to toggle source

Returns nucleic acid sequence length.

Returns | Integer

    # File lib/bio/db/kegg/genes.rb, line 411
    def ntlen
      fetch('NTSEQ')[/\d+/].to_i
    end

Also aliased as: nalen
ntseq() click to toggle source

Returns nucleic acid sequence described in the NTSEQ lines.

Returns | Bio::Sequence::NA object

    # File lib/bio/db/kegg/genes.rb, line 400
    def ntseq
      unless @data['NTSEQ']
        @data['NTSEQ'] = Bio::Sequence::NA.new(fetch('NTSEQ').gsub(/\d+/, ''))
      end
      @data['NTSEQ']
    end

Also aliased as: naseq
organism() click to toggle source

Organism name of the entry, described in the ENTRY line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 156
    def organism
      entry['organism']                   # H.sapiens etc.
    end

orthologs() click to toggle source
Alias for: orthologs_as_hash
orthologs_as_hash() click to toggle source

Returns a Hash of the orthology ID and definition in ORTHOLOGY field.

    # File lib/bio/db/kegg/genes.rb, line 107
    def orthologs_as_hash; super; end

Also aliased as: orthologs
orthologs_as_strings() click to toggle source

Orthologs described in the ORTHOLOGY lines.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 220
    def orthologs_as_strings
      lines_fetch('ORTHOLOGY')
    end

pathway() click to toggle source

Returns the PATHWAY lines as a String.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 227
    def pathway
      unless defined? @pathway
        @pathway = fetch('PATHWAY')
      end
      @pathway
    end

pathways() click to toggle source
Alias for: pathways_as_hash
pathways_as_hash() click to toggle source

Returns a Hash of the pathway ID and name in PATHWAY field.

    # File lib/bio/db/kegg/genes.rb, line 102
    def pathways_as_hash; super; end

Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathways described in the PATHWAY lines.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 237
    def pathways_as_strings
      lines_fetch('PATHWAY')
    end

position() click to toggle source

The position in the genome described in the POSITION line.

Returns | String

    # File lib/bio/db/kegg/genes.rb, line 254
    def position
      unless @data['POSITION']
        @data['POSITION'] = fetch('POSITION').gsub(/\s/, '')
      end
      @data['POSITION']
    end

structure() click to toggle source

Returns structure ID information described in the STRUCTURE lines.

Returns | Array containing String

    # File lib/bio/db/kegg/genes.rb, line 339
    def structure
      unless @data['STRUCTURE']
        @data['STRUCTURE'] = fetch('STRUCTURE').sub(/(PDB: )*/,'').split(/\s+/)
      end
      @data['STRUCTURE'] # ['PDB:1A9X', ...]
    end

Also aliased as: structures
structures() click to toggle source
Alias for: structure

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