bioinform 0.1.10 → 0.1.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: db3c7503656a2e0696ebf12a1259a9765864c50b
+  metadata.gz: 981be4ea2c5a07809303b9d4ac6a43f5d816e2f9
+  data.tar.gz: 84aa6ce722f015b357c1ac87cbb0151c8f37a3d2
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+  data.tar.gz: 45d806ad0a1befd381da35381f42d0cfcc1acd361bc35efa7ce9dacb203ab820e38564f8d93134ede8f5c380b1efc34ccc70ab1ee60ff7b3291c5ecc8d4e6c60

data/lib/bioinform/data_models/pwm.rb

@@ -23,14 +23,15 @@ module Bioinform
       raise ArgumentError, 'word in PWM#score(word) should have the same length as matrix'  unless word.length == length
       #raise ArgumentError, 'word in PWM#score(word) should have only ACGT-letters'  unless word.each_char.all?{|letter| %w{A C G T}.include? letter}
       (0...length).map do |pos|
-        begin
-        # Need support of N-letters and other IUPAC
-          letter = word[pos]
+        letter = word[pos]
+        if IndexByLetter[letter]
           matrix[pos][IndexByLetter[letter]]
-        rescue
-          raise ArgumentError, 'word in PWM#score(word) should have only ACGT-letters'
+        elsif letter == 'N'
+          matrix[pos].zip(probability).map{|el, p| el * p}.inject(0.0, &:+)
+        else
+          raise ArgumentError, "word in PWM#score(#{word}) should have only ACGT or N letters"
         end
-      end.inject(&:+)
+      end.inject(0.0, &:+)
     end
 
     def to_pwm

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
 module Bioinform
-  VERSION = "0.1.10"
+  VERSION = "0.1.11"
 end

data/spec/data_models/pwm_spec.rb

@@ -29,6 +29,10 @@ module Bioinform
         pwm.score('agata').should == 13141
         pwm.score('CCGCT').should == 22324
       end
+      it 'should give score average score(considering probabilities) for a position for a N-letter' do
+        pwm.score('AANAA').should == (11011 + 250)
+        pwm.set_parameters(background: [0.1,0.4,0.1,0.4]).score('AANAA').should == (11011 + 0.1*100 + 0.4*200 + 0.1*300 + 0.4*400)
+      end
       it 'should raise an ArgumentError if word contain bad letter' do
         expect{ pwm.score('AAAAV') }.to raise_error(ArgumentError)
       end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.1.10
+  version: 0.1.11
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-29 00:00:00.000000000 Z
+date: 2013-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport