# File lib/bio/db/kegg/genes.rb, line 83
83:   def initialize(entry)
84:     super(entry, TAGSIZE)
85:   end

     # File lib/bio/db/kegg/genes.rb, line 240
240:   def aalen
241:     fetch('AASEQ')[/\d+/].to_i
242:   end

     # File lib/bio/db/kegg/genes.rb, line 233
233:   def aaseq
234:     unless @data['AASEQ']
235:       @data['AASEQ'] = Bio::Sequence::AA.new(fetch('AASEQ').gsub(/\d+/, ''))
236:     end
237:     @data['AASEQ']
238:   end

     # File lib/bio/db/kegg/genes.rb, line 158
158:   def chromosome
159:     if position[/:/]
160:       position.sub(/:.*/, '')
161:     elsif ! position[/\.\./]
162:       position
163:     else
164:       nil
165:     end
166:   end

     # File lib/bio/db/kegg/genes.rb, line 206
206:   def codon_usage(codon = nil)
207:     unless @data['CODON_USAGE']
208:       hash = Hash.new
209:       list = cu_list
210:       base = %w(t c a g)
211:       base.each_with_index do |x, i|
212:         base.each_with_index do |y, j|
213:           base.each_with_index do |z, k|
214:             hash["#{x}#{y}#{z}"] = list[i*16 + j*4 + k]
215:           end
216:         end
217:       end
218:       @data['CODON_USAGE'] = hash
219:     end
220:     @data['CODON_USAGE']
221:   end

     # File lib/bio/db/kegg/genes.rb, line 223
223:   def cu_list
224:     ary = []
225:     get('CODON_USAGE').sub(/.*/,'').each_line do |line| # cut 1st line
226:       line.chomp.sub(/^.{11}/, '').scan(/..../) do |cu|
227:         ary.push(cu.to_i)
228:       end
229:     end
230:     return ary
231:   end

     # File lib/bio/db/kegg/genes.rb, line 194
194:   def dblinks
195:     unless @data['DBLINKS']
196:       hash = {}
197:       get('DBLINKS').scan(/(\S+):\s*(.*)\n?/).each do |db, str|
198:         id_array = str.strip.split(/\s+/)
199:         hash[db] = id_array
200:       end
201:       @data['DBLINKS'] = hash
202:     end
203:     @data['DBLINKS']            # Hash of Array of IDs in DBLINKS
204:   end

     # File lib/bio/db/kegg/genes.rb, line 126
126:   def definition
127:     field_fetch('DEFINITION')
128:   end

     # File lib/bio/db/kegg/genes.rb, line 106
106:   def division
107:     entry['division']                   # CDS, tRNA etc.
108:   end

     # File lib/bio/db/kegg/genes.rb, line 130
130:   def eclinks
131:     ec_list = definition.slice(/\[EC:(.*?)\]/, 1)
132:     if ec_list
133:       ec_list.strip.split(/\s+/)
134:     else
135:       []
136:     end
137:   end

     # File lib/bio/db/kegg/genes.rb, line 88
 88:   def entry
 89:     unless @data['ENTRY']
 90:       hash = Hash.new('')
 91:       if get('ENTRY').length > 30
 92:         e = get('ENTRY')
 93:         hash['id']       = e[12..29].strip
 94:         hash['division'] = e[30..39].strip
 95:         hash['organism'] = e[40..80].strip
 96:       end
 97:       @data['ENTRY'] = hash
 98:     end
 99:     @data['ENTRY']
100:   end

     # File lib/bio/db/kegg/genes.rb, line 102
102:   def entry_id
103:     entry['id']
104:   end

     # File lib/bio/db/kegg/genes.rb, line 168
168:   def gbposition
169:     position.sub(/.*?:/, '')
170:   end

     # File lib/bio/db/kegg/genes.rb, line 122
122:   def gene
123:     genes.first
124:   end

     # File lib/bio/db/kegg/genes.rb, line 118
118:   def genes
119:     name.split(', ')
120:   end

     # File lib/bio/db/kegg/genes.rb, line 172
172:   def locations
173:     Bio::Locations.new(gbposition)
174:   end

     # File lib/bio/db/kegg/genes.rb, line 176
176:   def motif
177:     unless @data['MOTIF']
178:       hash = {}
179:       db = nil
180:       lines_fetch('MOTIF').each do |line|
181:         if line[/^\S+:/]
182:           db, str = line.split(/:/)
183:         else
184:           str = line
185:         end
186:         hash[db] ||= []
187:         hash[db] += str.strip.split(/\s+/)
188:       end
189:       @data['MOTIF'] = hash
190:     end
191:     @data['MOTIF']              # Hash of Array of IDs in MOTIF
192:   end

     # File lib/bio/db/kegg/genes.rb, line 114
114:   def name
115:     field_fetch('NAME')
116:   end

     # File lib/bio/db/kegg/genes.rb, line 252
252:   def ntlen
253:     fetch('NTSEQ')[/\d+/].to_i
254:   end

     # File lib/bio/db/kegg/genes.rb, line 244
244:   def ntseq
245:     unless @data['NTSEQ']
246:       @data['NTSEQ'] = Bio::Sequence::NA.new(fetch('NTSEQ').gsub(/\d+/, ''))
247:     end
248:     @data['NTSEQ']
249:   end

     # File lib/bio/db/kegg/genes.rb, line 110
110:   def organism
111:     entry['organism']                   # H.sapiens etc.
112:   end

     # File lib/bio/db/kegg/genes.rb, line 139
139:   def orthologs
140:     lines_fetch('ORTHOLOGY')
141:   end

     # File lib/bio/db/kegg/genes.rb, line 143
143:   def pathway
144:     field_fetch('PATHWAY')
145:   end

     # File lib/bio/db/kegg/genes.rb, line 147
147:   def pathways
148:     pathway.scan(/\[PATH:(.*?)\]/).flatten
149:   end

     # File lib/bio/db/kegg/genes.rb, line 151
151:   def position
152:     unless @data['POSITION']
153:       @data['POSITION'] = fetch('POSITION').gsub(/\s/, '')
154:     end
155:     @data['POSITION']
156:   end