class Bio::KEGG::GENOME
Description¶ ↑
Parser for the KEGG
GENOME
database
References
¶ ↑
Constants
- DELIMITER
- TAGSIZE
Public Class Methods
Bio::NCBIDB::new
# File lib/bio/db/kegg/genome.rb 38 def initialize(entry) 39 super(entry, TAGSIZE) 40 end
Public Instance Methods
CHROMOSOME – Returns contents of the CHROMOSOME records as an Array of Hash.
# File lib/bio/db/kegg/genome.rb 140 def chromosomes 141 unless @data['CHROMOSOME'] 142 @data['CHROMOSOME'] = [] 143 toptag2array(get('CHROMOSOME')).each do |chr| 144 hash = Hash.new('') 145 subtag2array(chr).each do |field| 146 hash[tag_get(field)] = truncate(tag_cut(field)) 147 end 148 @data['CHROMOSOME'].push(hash) 149 end 150 end 151 @data['CHROMOSOME'] 152 end
COMMENT – Returns contents of the COMMENT record as a String.
# File lib/bio/db/kegg/genome.rb 134 def comment 135 field_fetch('COMMENT') 136 end
DATA_SOURCE – Returns contents of the DATA_SOURCE record as a String.
# File lib/bio/db/kegg/genome.rb 106 def data_source 107 field_fetch('DATA_SOURCE') 108 end
DEFINITION – Returns contents of the DEFINITION record as a String.
# File lib/bio/db/kegg/genome.rb 75 def definition 76 field_fetch('DEFINITION') 77 end
DISEASE – Returns contents of the COMMENT record as a String.
# File lib/bio/db/kegg/genome.rb 129 def disease 130 field_fetch('DISEASE') 131 end
ENTRY – Returns contents of the ENTRY record as a String.
# File lib/bio/db/kegg/genome.rb 65 def entry_id 66 field_fetch('ENTRY')[/\S+/] 67 end
Returns contents of the TAXONOMY/LINEAGE record as a String.
# File lib/bio/db/kegg/genome.rb 101 def lineage 102 taxonomy['lineage'] 103 end
Returns number of nucleotides from the STATISTICS record as a Fixnum.
# File lib/bio/db/kegg/genome.rb 189 def nalen 190 statistics['num_nuc'] 191 end
NAME – Returns contents of the NAME record as a String.
# File lib/bio/db/kegg/genome.rb 70 def name 71 field_fetch('NAME') 72 end
Returns number of protein genes from the STATISTICS record as a Fixnum.
# File lib/bio/db/kegg/genome.rb 195 def num_gene 196 statistics['num_gene'] 197 end
Returns number of rna from the STATISTICS record as a Fixnum.
# File lib/bio/db/kegg/genome.rb 200 def num_rna 201 statistics['num_rna'] 202 end
Returns ORIGINAL_DB record as an Array containing String objects.
Arguments:
- Returns
-
Array containing String objects
# File lib/bio/db/kegg/genome.rb 124 def original_databases 125 lines_fetch('ORIGINAL_DB') 126 end
ORIGINAL_DB – Returns contents of the ORIGINAL_DB record as a String.
# File lib/bio/db/kegg/genome.rb 111 def original_db 112 #field_fetch('ORIGINAL_DB') 113 unless defined?(@original_db) 114 @original_db = fetch('ORIGINAL_DB') 115 end 116 @original_db 117 end
PLASMID – Returns contents of the PLASMID records as an Array of Hash.
# File lib/bio/db/kegg/genome.rb 155 def plasmids 156 unless @data['PLASMID'] 157 @data['PLASMID'] = [] 158 toptag2array(get('PLASMID')).each do |chr| 159 hash = Hash.new('') 160 subtag2array(chr).each do |field| 161 hash[tag_get(field)] = truncate(tag_cut(field)) 162 end 163 @data['PLASMID'].push(hash) 164 end 165 end 166 @data['PLASMID'] 167 end
REFERENCE – Returns contents of the REFERENCE records as an Array of Bio::Reference
objects.
Bio::KEGG::Common::References#references
# File lib/bio/db/kegg/genome.rb 35 def references; super; end
STATISTICS – Returns contents of the STATISTICS record as a Hash.
# File lib/bio/db/kegg/genome.rb 170 def statistics 171 unless @data['STATISTICS'] 172 hash = Hash.new(0.0) 173 get('STATISTICS').each_line do |line| 174 case line 175 when /nucleotides:\s+(\d+)/ 176 hash['num_nuc'] = $1.to_i 177 when /protein genes:\s+(\d+)/ 178 hash['num_gene'] = $1.to_i 179 when /RNA genes:\s+(\d+)/ 180 hash['num_rna'] = $1.to_i 181 end 182 end 183 @data['STATISTICS'] = hash 184 end 185 @data['STATISTICS'] 186 end
Returns NCBI
taxonomy ID from the TAXONOMY record as a String.
# File lib/bio/db/kegg/genome.rb 96 def taxid 97 taxonomy['taxid'] 98 end
TAXONOMY – Returns contents of the TAXONOMY record as a Hash.
# File lib/bio/db/kegg/genome.rb 81 def taxonomy 82 unless @data['TAXONOMY'] 83 taxid, lineage = subtag2array(get('TAXONOMY')) 84 taxid = taxid ? truncate(tag_cut(taxid)) : '' 85 lineage = lineage ? truncate(tag_cut(lineage)) : '' 86 @data['TAXONOMY'] = { 87 'taxid' => taxid, 88 'lineage' => lineage, 89 } 90 @data['TAXONOMY'].default = '' 91 end 92 @data['TAXONOMY'] 93 end