vienna_rna 0.1.6 → 0.1.7

data/lib/vienna_rna/modules/base.rb

@@ -24,6 +24,12 @@ module ViennaRna
         new(data).run(flags)
       end
       
+      def bootstrap(data, output)
+        new(data).tap do |object|
+          object.instance_variable_set(:@response, output)
+        end
+      end
+      
       def batch(fastas = [])
         ViennaRna::Batch.new(self, fastas).tap do |batch|
           if const_defined?(:Batch)

data/lib/vienna_rna/modules/rna.rb

@@ -3,7 +3,7 @@ module ViennaRna
     attr_reader :sequence, :structure
       
     def initialize(sequence, structure = nil)
-      @sequence  = sequence
+      @sequence  = sequence.upcase
       @structure = (structure == :mfe ? ViennaRna::Fold.run(seq).structure : structure)
     end
 
@@ -17,5 +17,73 @@ module ViennaRna
     def empty_structure
       "." * seq.length
     end
+    
+    def bp_distance(other_structure)
+      self.class.bp_distance(structure, other_structure)
+    end
+    
+    def base_pairs
+      self.class.base_pairs(structure)
+    end
+            
+    def get_pairings
+      self.class.get_pairings(structure)
+    end
+    
+    def dishuffle
+      self.class.shuffle(sequence, 2)
+    end
+    
+    def inspect
+      "#<ViennaRna::#{self.class.name} #{seq[0, 20] + ('...' if seq.length > 20)} #{str[0, 20] + ('[truncated]' if seq.length > 20)}>"
+    end
+    
+    class << self
+      def generate_sequence(sequence_length)
+        # 0th order Markov chain w/ uniform probability distribution
+        sequence_length.times.inject("") { |string, _| string + %w[A U C G][rand(4)] }
+      end
+      
+      def shuffle(sequence, token_length = 2)
+        Shuffle.new(sequence).shuffle(token_length)
+      end
+      
+      def bp_distance(structure_1, structure_2)
+        raise "The two structures are not the same length" unless structure_1.length == structure_2.length
+        
+        bp_set_1, bp_set_2 = base_pairs(structure_1), base_pairs(structure_2)
+        
+        ((bp_set_1 - bp_set_2) + (bp_set_2 - bp_set_1)).count
+      end
+      
+      def base_pairs(structure)
+        get_pairings(structure).each_with_index.inject(Set.new) do |set, (j, i)|
+          j >= 0 ? set << Set[i, j] : set
+        end
+      end
+    
+      def get_pairings(structure)
+      	stack = []
+      
+        structure.each_char.each_with_index.inject(Array.new(structure.length, -1)) do |array, (symbol, index)|
+      	  array.tap do      
+      	    case symbol
+      	    when "(" then stack.push(index)
+      	    when ")" then 
+      	      if stack.empty?
+      	        raise "Too many ')' in '#{structure}'"
+      	      else
+      	        stack.pop.tap do |opening|
+      	          array[opening] = index
+      	          array[index]   = opening
+      	        end
+      	      end
+      	    end
+      	  end
+      	end.tap do
+      	  raise "Too many '(' in '#{structure}'" unless stack.empty?
+      	end
+      end
+    end
   end
 end

data/lib/vienna_rna/modules/utils.rb

@@ -1,6 +1,3 @@
-require "matrix"
-require "gnuplot"
-
 module ViennaRna
   module Utils
     class << self
@@ -57,11 +54,15 @@ module ViennaRna
       end
       
       def quick_plot(title, data, filename = false)
-        # data = [[x_0, y_0], [x_1, y_1], ...]        
+        quick_overlay(title, [{ data: data }], filename)
+      end
+      
+      def quick_overlay(title, data, filename = false)
+        # [{ data: [[x_0, y_0], [x_1, y_1], ...], label: "Label" }, { data: [[x_0, y_0], [x_1, y_1], ...] }]
         options = { title: title }
         options.merge!(output: "file", filename: filename) if filename
         
-        plot([{ x: data.map(&:first), y: data.map(&:last), style: "linespoints" }], options)
+        plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[:data].map(&:last), style: "linespoints" } }, options)
       end
     end
   end

data/lib/vienna_rna/modules/xbor.rb

@@ -35,11 +35,19 @@ module ViennaRna
       full_distribution.each_with_index.to_a.map(&:reverse)[0..data.seq.length]
     end
     
+    def expected_k
+      k_p_points.map { |array| array.inject(&:*) }.inject(&:+)
+    end
+    
     def quick_plot(title = nil)
       ViennaRna::Utils.quick_plot(
         title || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure], 
         k_p_points
       )
     end
+    
+    def inspect
+      "#<ViennaRna::#{self.class.name} #{data.inspect}>"
+    end
   end
 end

data/lib/vienna_rna.rb

@@ -1,4 +1,8 @@
+require "set"
 require "bio"
+require "shuffle"
+require "matrix"
+require "gnuplot"
 require "active_support/inflector"
 require "active_support/core_ext/class"
 require "active_support/core_ext/module/aliasing"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.6
+  version: 0.1.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-15 00:00:00.000000000 Z
+date: 2012-09-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -34,7 +34,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 3.2.5
+        version: '3.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -42,7 +42,39 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 3.2.5
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: shuffle
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: gnuplot
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.5.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 2.5.0
 description: A Ruby API for interacting with the Vienna RNA package.
 email: evansenter@gmail.com
 executables: []