Class: Bio::KEGG::GENOME

    # File lib/bio/db/kegg/genome.rb, line 28
28:   def initialize(entry)
29:     super(entry, TAGSIZE)
30:   end

chromosomes()

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

[Source]

     # File lib/bio/db/kegg/genome.rb, line 133
133:   def chromosomes
134:     unless @data['CHROMOSOME']
135:       @data['CHROMOSOME'] = []
136:       toptag2array(get('CHROMOSOME')).each do |chr|
137:         hash = Hash.new('')
138:         subtag2array(chr).each do |field|
139:           hash[tag_get(field)] = truncate(tag_cut(field))
140:         end
141:         @data['CHROMOSOME'].push(hash)
142:       end
143:     end
144:     @data['CHROMOSOME']
145:   end

comment()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 90
90:   def comment
91:     field_fetch('COMMENT')
92:   end

data_source()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 75
75:   def data_source
76:     field_fetch('DATA_SOURCE')
77:   end

definition()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 44
44:   def definition
45:     field_fetch('DEFINITION')
46:   end

disease()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 85
85:   def disease
86:     field_fetch('DISEASE')
87:   end

entry_id()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 34
34:   def entry_id
35:     field_fetch('ENTRY')[/\S+/]
36:   end

length()

Alias for nalen

lineage()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 70
70:   def lineage
71:     taxonomy['lineage']
72:   end

nalen()

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

[Source]

     # File lib/bio/db/kegg/genome.rb, line 182
182:   def nalen
183:     statistics['num_nuc']
184:   end

name()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 39
39:   def name
40:     field_fetch('NAME')
41:   end

num_gene()

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

[Source]

     # File lib/bio/db/kegg/genome.rb, line 188
188:   def num_gene
189:     statistics['num_gene']
190:   end

num_rna()

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

[Source]

     # File lib/bio/db/kegg/genome.rb, line 193
193:   def num_rna
194:     statistics['num_rna']
195:   end

organism()

Alias for definition

original_db()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 80
80:   def original_db
81:     field_fetch('ORIGINAL_DB')
82:   end

plasmids()

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

[Source]

     # File lib/bio/db/kegg/genome.rb, line 148
148:   def plasmids
149:     unless @data['PLASMID']
150:       @data['PLASMID'] = []
151:       toptag2array(get('PLASMID')).each do |chr|
152:         hash = Hash.new('')
153:         subtag2array(chr).each do |field|
154:           hash[tag_get(field)] = truncate(tag_cut(field))
155:         end
156:         @data['PLASMID'].push(hash)
157:       end
158:     end
159:     @data['PLASMID']
160:   end

references()

REFERENCE — Returns contents of the REFERENCE records as an Array of Bio::Reference objects.

[Source]

     # File lib/bio/db/kegg/genome.rb, line 96
 96:   def references
 97:     unless @data['REFERENCE']
 98:       ary = []
 99:       toptag2array(get('REFERENCE')).each do |ref|
100:         hash = Hash.new('')
101:         subtag2array(ref).each do |field|
102:           case tag_get(field)
103:           when /AUTHORS/
104:             authors = truncate(tag_cut(field))
105:             authors = authors.split(', ')
106:             authors[-1] = authors[-1].split(/\s+and\s+/)
107:             authors = authors.flatten.map { |a| a.sub(',', ', ') }
108:             hash['authors']     = authors
109:           when /TITLE/
110:             hash['title']       = truncate(tag_cut(field))
111:           when /JOURNAL/
112:             journal = truncate(tag_cut(field))
113:             if journal =~ /(.*) (\d+):(\d+)-(\d+) \((\d+)\) \[UI:(\d+)\]$/
114:               hash['journal']   = $1
115:               hash['volume']    = $2
116:               hash['pages']     = $3
117:               hash['year']      = $5
118:               hash['medline']   = $6
119:             else
120:               hash['journal'] = journal
121:             end
122:           end
123:         end
124:         ary.push(Reference.new(hash))
125:       end
126:       @data['REFERENCE'] = References.new(ary)
127:     end
128:     @data['REFERENCE']
129:   end

statistics()

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

[Source]

     # File lib/bio/db/kegg/genome.rb, line 163
163:   def statistics
164:     unless @data['STATISTICS']
165:       hash = Hash.new(0.0)
166:       get('STATISTICS').each_line do |line|
167:         case line
168:         when /nucleotides:\s+(\d+)/
169:           hash['num_nuc'] = $1.to_i
170:         when /protein genes:\s+(\d+)/
171:           hash['num_gene'] = $1.to_i
172:         when /RNA genes:\s+(\d+)/
173:           hash['num_rna'] = $1.to_i
174:         end
175:       end
176:       @data['STATISTICS'] = hash
177:     end
178:     @data['STATISTICS']
179:   end

taxid()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 65
65:   def taxid
66:     taxonomy['taxid']
67:   end

taxonomy()

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

[Source]

    # File lib/bio/db/kegg/genome.rb, line 50
50:   def taxonomy
51:     unless @data['TAXONOMY']
52:       taxid, lineage = subtag2array(get('TAXONOMY'))
53:       taxid   = taxid   ? truncate(tag_cut(taxid))   : ''
54:       lineage = lineage ? truncate(tag_cut(lineage)) : ''
55:       @data['TAXONOMY'] = {
56:         'taxid' => taxid,
57:         'lineage'       => lineage,
58:       }
59:       @data['TAXONOMY'].default = ''
60:     end
61:     @data['TAXONOMY']
62:   end

Description

References

Methods

Constants

Public Class methods

Public Instance methods

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