class Bio::AAindex1

Description

Parser class for AAindex1, Amino Acid Index Database.

Examples

# auto-detection of data format by using Bio::AAindex class
aax1 = Bio::AAindex.auto("PRAM900102.aaindex1")

# parse a file and get contents
aax1 = Bio::AAindex1.new("PRAM900102.aaindex1")
aax1.entry_id
aax1.index

References

Public Class Methods

new(entry) click to toggle source
Calls superclass method Bio::AAindex::new
    # File lib/bio/db/aaindex.rb
190 def initialize(entry)
191   super(entry)
192 end

Public Instance Methods

correlation_coefficient() click to toggle source

Returns correlation_coefficient (Hash) in the C line.

cf.) {'ABCD12010203' => 0.999, 'CDEF123456' => 0.543, …}

    # File lib/bio/db/aaindex.rb
197 def correlation_coefficient
198   if @data['correlation_coefficient']
199     @data['correlation_coefficient']
200   else
201     hash = {}
202     ary = field_fetch('C').split(' ')
203     ary.each do |x|
204       next unless x =~ /^[A-Z]/
205       hash[x] = ary[ary.index(x) + 1].to_f
206     end
207     @data['correlation_coefficient'] = hash
208   end
209 end
index(type = :float) click to toggle source

Returns the index (Array) in the I line.

an argument: :string, :float, :zscore or :integer

    # File lib/bio/db/aaindex.rb
214 def index(type = :float)
215   aa = %w( A R N D C Q E G H I L K M F P S T W Y V )
216   values = field_fetch('I', 1).split(' ')
217 
218   if values.size != 20
219     raise "Invalid format in #{entry_id} : #{values.inspect}"
220   end
221 
222   if type == :zscore and values.size > 0
223     sum = 0.0
224     values.each do |a|
225       sum += a.to_f
226     end
227     mean = sum / values.size # / 20
228     var = 0.0
229     values.each do |a|
230       var += (a.to_f - mean) ** 2
231     end
232     sd = Math.sqrt(var)
233   end
234 
235   if type == :integer
236     figure = 0
237     values.each do |a|
238       figure = [ figure, a[/\..*/].length - 1 ].max
239     end
240   end
241 
242   hash = {}
243 
244   aa.each_with_index do |a, i|
245     case type
246     when :string
247       hash[a] = values[i]
248     when :float
249       hash[a] = values[i].to_f
250     when :zscore
251       hash[a] = (values[i].to_f - mean) / sd
252     when :integer
253       hash[a] = (values[i].to_f * 10 ** figure).to_i
254     end
255   end
256   return hash
257 end