Module Bio::NucleicAcid::Data
In: lib/bio/data/na.rb

Methods

[]   na   name   names   to_re   weight  

Constants

NAMES = { 'y' => '[tc]', 'r' => '[ag]', 'w' => '[at]', 's' => '[gc]', 'k' => '[tg]', 'm' => '[ac]', 'b' => '[tgc]', 'd' => '[atg]', 'h' => '[atc]', 'v' => '[agc]', 'n' => '[atgc]', 'a' => 'a', 't' => 't', 'g' => 'g', 'c' => 'c', 'u' => 'u', 'A' => 'Adenine', 'T' => 'Thymine', 'G' => 'Guanine', 'C' => 'Cytosine', 'U' => 'Uracil', 'Y' => 'pYrimidine', 'R' => 'puRine', 'W' => 'Weak', 'S' => 'Strong', 'K' => 'Keto', 'M' => 'aroMatic', 'B' => 'not A', 'D' => 'not C', 'H' => 'not G', 'V' => 'not T', }   IUPAC code
WEIGHT = { # Calculated by BioPerl's Bio::Tools::SeqStats.pm :-) 'a' => 135.15, 't' => 126.13, 'g' => 151.15, 'c' => 111.12, 'u' => 112.10, :adenine => 135.15, :thymine => 126.13, :guanine => 151.15, :cytosine => 111.12, :uracil => 112.10, :deoxyribose_phosphate => 196.11, :ribose_phosphate => 212.11, :hydrogen => 1.00794, :water => 18.015, }

Public Instance methods

[](x)

[Source]

     # File lib/bio/data/na.rb, line 146
146:     def [](x)
147:       NAMES[x]
148:     end
na()

Alias for names

name(x)

[Source]

     # File lib/bio/data/na.rb, line 156
156:     def name(x)
157:       NAMES[x.to_s.upcase]
158:     end
names()

backward compatibility

[Source]

     # File lib/bio/data/na.rb, line 151
151:     def names
152:       NAMES
153:     end
to_re(seq, rna = false)

[Source]

     # File lib/bio/data/na.rb, line 160
160:     def to_re(seq, rna = false)
161:       replace = {
162:         'y' => '[tcy]',
163:         'r' => '[agr]',
164:         'w' => '[atw]',
165:         's' => '[gcw]',
166:         'k' => '[tgk]',
167:         'm' => '[acm]',
168:         'b' => '[tgcyskb]',
169:         'd' => '[atgrwkd]',
170:         'h' => '[atcwmyh]',
171:         'v' => '[agcmrsv]',
172:         'n' => '[atgcyrwskmbdhvn]'
173:       }
174:       replace.default = '.'
175: 
176:       str = seq.to_s.downcase
177:       str.gsub!(/[^atgcu]/) { |na|
178:         replace[na]
179:       }
180:       if rna
181:         str.tr!("t", "u")
182:       end
183:       Regexp.new(str)
184:     end
weight(x = nil, rna = nil)

[Source]

     # File lib/bio/data/na.rb, line 117
117:     def weight(x = nil, rna = nil)
118:       if x
119:         if x.length > 1
120:           if rna
121:             phosphate = WEIGHT[:ribose_phosphate]
122:           else
123:             phosphate = WEIGHT[:deoxyribose_phosphate]
124:           end
125:           hydrogen    = WEIGHT[:hydrogen]
126:           water       = WEIGHT[:water]
127: 
128:           total = 0.0
129:           x.each_byte do |byte|
130:             base = byte.chr.downcase
131:             if WEIGHT[base]
132:               total += WEIGHT[base] + phosphate - hydrogen * 2
133:             else
134:               raise "Error: invalid nucleic acid '#{base}'"
135:             end
136:           end
137:           total -= water * (x.length - 1)
138:         else
139:           WEIGHT[x.to_s.downcase]
140:         end
141:       else
142:         WEIGHT
143:       end
144:     end

[Validate]