vienna_rna 0.0.4 → 0.0.5

data/lib/modules/base.rb

@@ -70,11 +70,15 @@ module ViennaRna
     end
     
     def run(flags = {})
-      if respond_to?(:run_command)
-        %x[#{method(:run_command).arity.zero? ? run_command : run_command(flags)}]
+      command = if respond_to?(:run_command)
+        method(:run_command).arity.zero? ? run_command : run_command(flags)
       else
-        %x[echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}]
+        "echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}"
       end
+      
+      puts command if ViennaRna.debug
+        
+      %x[#{command}]
     end
   end
 end

data/lib/modules/fft_in_r.rb

@@ -0,0 +1,26 @@
+module ViennaRna
+  class FftInR < Base
+    attr_reader :processed_response, :points, :total_count, :precision
+    
+    def initialize(points, total_count, precision)
+      @points      = points
+      @total_count = total_count
+      @precision   = precision
+    end
+    
+    def run_command
+      vector = "c(%s)" % points.map { |point| 10 ** precision * point / total_count }.join(", ")
+      "Rscript -e 'vector <- #{vector}; fft(vector) / length(vector);'" % vector
+    end
+    
+    def post_process
+      @processed_response = response.split(/\n/).map do |line| 
+        line.strip.match(/\[\d+\]\s+(.*)$/)[1].split(/\s+/)
+      end.flatten.map do |i|
+        i.match(/(-?\d+\.\d+e[\+-]\d+)/)[1].to_f
+      end.map do |i|
+        precision.zero? ? i : i.truncate / 10.0 ** precision
+      end
+    end
+  end
+end

data/lib/modules/rnabor.rb

@@ -1,7 +1,7 @@
 module ViennaRna
   class Rnabor < Base
     def run_command(flags)
-      "./RNAbor -s %s -c %s" % [fasta.seq, flags[:scaling_factor]]
+      "./RNAbor -s %s -c %s" % [fasta.seq, flags[:scaling_factor] || 1]
     end
     
     def parse_total_count
@@ -16,6 +16,20 @@ module ViennaRna
       self.class.parse(response, "UNSCALED SUM") { |line| line.strip.split(/:\s*/).map(&:to_f) }
     end
     
+    def in_r(options = {})
+      results = solve_in_r(options).processed_response
+      
+      options[:unscale] ? results.map { |i| i * parse_total_count } : results
+    end
+    
+    def solve_in_r(options = {})
+      options = { precision: 0, unscale: false }.merge(options)
+      
+      run unless response
+      
+      ViennaRna::FftInR.new(parse_points.map(&:last), parse_total_count, options[:precision]).run
+    end
+    
     def self.parse(response, delimiter)
       response.split(/\n/).reject do |line| 
         line.empty?

data/lib/vienna_rna.rb

@@ -8,7 +8,15 @@ Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
   require file
 end
 
+module Enumerable
+  def sum
+    inject { |sum, i| sum + i }
+  end
+end
+
 module ViennaRna
+  @debug = false
+  
   def self.const_missing(name)
     if Base.exec_exists?(name)
       module_eval do
@@ -16,4 +24,12 @@ module ViennaRna
       end
     end
   end
+  
+  def self.debug
+    @debug
+  end
+  
+  def self.debug=(value)
+    @debug = value
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors:
@@ -18,7 +18,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
@@ -53,6 +53,8 @@ files:
   Li9saWIvbW9kdWxlcy9iYXNlLnJi
 - !binary |-
   Li9saWIvbW9kdWxlcy9iYXRjaC5yYg==
+- !binary |-
+  Li9saWIvbW9kdWxlcy9mZnRfaW5fci5yYg==
 - !binary |-
   Li9saWIvbW9kdWxlcy9mb2xkLnJi
 - !binary |-