Class: Bio::KEGG::GENOME

Inherits:
Bio::KEGGDB show all
Includes:
Common::References
Defined in:
lib/bio/db/kegg/genome.rb

Overview

Constant Summary

DELIMITER =
RS = "\n///\n"
TAGSIZE =
12

Instance Method Summary (collapse)

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

- (GENOME) initialize(entry)

Returns a new instance of GENOME



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# File 'lib/bio/db/kegg/genome.rb', line 38

def initialize(entry)
  super(entry, TAGSIZE)
end

Instance Method Details

- (Object) chromosomes

CHROMOSOME – Returns contents of the CHROMOSOME records as an Array of Hash.



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# File 'lib/bio/db/kegg/genome.rb', line 140

def chromosomes
  unless @data['CHROMOSOME']
    @data['CHROMOSOME'] = []
    toptag2array(get('CHROMOSOME')).each do |chr|
      hash = Hash.new('')
      subtag2array(chr).each do |field|
        hash[tag_get(field)] = truncate(tag_cut(field))
      end
      @data['CHROMOSOME'].push(hash)
    end
  end
  @data['CHROMOSOME']
end

- (Object) comment

COMMENT – Returns contents of the COMMENT record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 134

def comment
  field_fetch('COMMENT')
end

- (Object) data_source

DATA_SOURCE – Returns contents of the DATA_SOURCE record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 106

def data_source
  field_fetch('DATA_SOURCE')
end

- (Object) definition Also known as: organism

DEFINITION – Returns contents of the DEFINITION record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 75

def definition
  field_fetch('DEFINITION')
end

- (Object) disease

DISEASE – Returns contents of the COMMENT record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 129

def disease
  field_fetch('DISEASE')
end

- (Object) entry_id

ENTRY – Returns contents of the ENTRY record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 65

def entry_id
  field_fetch('ENTRY')[/\S+/]
end

- (Object) lineage

Returns contents of the TAXONOMY/LINEAGE record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 101

def lineage
  taxonomy['lineage']
end

- (Object) nalen Also known as: length

Returns number of nucleotides from the STATISTICS record as a Fixnum.



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# File 'lib/bio/db/kegg/genome.rb', line 189

def nalen
  statistics['num_nuc']
end

- (Object) name

NAME – Returns contents of the NAME record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 70

def name
  field_fetch('NAME')
end

- (Object) num_gene

Returns number of protein genes from the STATISTICS record as a Fixnum.



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# File 'lib/bio/db/kegg/genome.rb', line 195

def num_gene
  statistics['num_gene']
end

- (Object) num_rna

Returns number of rna from the STATISTICS record as a Fixnum.



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# File 'lib/bio/db/kegg/genome.rb', line 200

def num_rna
  statistics['num_rna']
end

- (Object) original_databases

Returns ORIGINAL_DB record as an Array containing String objects.


Arguments:

Returns

Array containing String objects



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# File 'lib/bio/db/kegg/genome.rb', line 124

def original_databases
  lines_fetch('ORIGINAL_DB')
end

- (Object) original_db

ORIGINAL_DB – Returns contents of the ORIGINAL_DB record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 111

def original_db
  #field_fetch('ORIGINAL_DB')
  unless defined?(@original_db)
    @original_db = fetch('ORIGINAL_DB')
  end
  @original_db
end

- (Object) plasmids

PLASMID – Returns contents of the PLASMID records as an Array of Hash.



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# File 'lib/bio/db/kegg/genome.rb', line 155

def plasmids
  unless @data['PLASMID']
    @data['PLASMID'] = []
    toptag2array(get('PLASMID')).each do |chr|
      hash = Hash.new('')
      subtag2array(chr).each do |field|
        hash[tag_get(field)] = truncate(tag_cut(field))
      end
      @data['PLASMID'].push(hash)
    end
  end
  @data['PLASMID']
end

- (Object) references



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# File 'lib/bio/db/kegg/genome.rb', line 35

def references; super; end

- (Object) statistics

STATISTICS – Returns contents of the STATISTICS record as a Hash.



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# File 'lib/bio/db/kegg/genome.rb', line 170

def statistics
  unless @data['STATISTICS']
    hash = Hash.new(0.0)
    get('STATISTICS').each_line do |line|
      case line
      when /nucleotides:\s+(\d+)/
        hash['num_nuc'] = $1.to_i
      when /protein genes:\s+(\d+)/
        hash['num_gene'] = $1.to_i
      when /RNA genes:\s+(\d+)/
        hash['num_rna'] = $1.to_i
      end
    end
    @data['STATISTICS'] = hash
  end
  @data['STATISTICS']
end

- (Object) taxid

Returns NCBI taxonomy ID from the TAXONOMY record as a String.



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# File 'lib/bio/db/kegg/genome.rb', line 96

def taxid
  taxonomy['taxid']
end

- (Object) taxonomy

TAXONOMY – Returns contents of the TAXONOMY record as a Hash.



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# File 'lib/bio/db/kegg/genome.rb', line 81

def taxonomy
  unless @data['TAXONOMY']
    taxid, lineage = subtag2array(get('TAXONOMY'))
    taxid   = taxid   ? truncate(tag_cut(taxid))   : ''
    lineage = lineage ? truncate(tag_cut(lineage)) : ''
    @data['TAXONOMY'] = {
      'taxid'	=> taxid,
      'lineage'	=> lineage,
    }
    @data['TAXONOMY'].default = ''
  end
  @data['TAXONOMY']
end