vienna_rna 0.1.0 → 0.1.1

data/lib/modules/base.rb

@@ -52,12 +52,20 @@ module ViennaRna
           end
         end
       end
+      
+      def debugger
+        STDERR.puts yield if ViennaRna.debug
+      end
     end
     
     attr_reader :data, :response, :runtime
     
     def exec_name
-      executable_name || "rna#{self.class.name.split('::').last.underscore}"
+      if executable_name
+        executable_name.respond_to?(:call) ? self.class.module_exec(&executable_name) : executable_name
+      else
+        "rna#{self.class.name.split('::').last.underscore}"
+      end
     end
     
     def exec_sequence_format
@@ -80,7 +88,7 @@ module ViennaRna
           post_process if respond_to?(:post_process)
         end
         
-        puts "Total runtime: %.3f sec." % runtime.real if ViennaRna.debug
+        debugger { "Total runtime: %.3f sec." % runtime.real }
       end
     end
     
@@ -101,9 +109,13 @@ module ViennaRna
         "echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}"
       end
       
-      puts command if ViennaRna.debug
+      debugger { command }
         
       %x[#{command}]
     end
+    
+    def debugger(&block)
+      self.class.debugger(&block)
+    end
   end
 end

data/lib/modules/fftbor.rb

@@ -1,20 +1,11 @@
 require "tempfile"
+require "bigdecimal"
 
 module ViennaRna
-  class Fftbor < Base
-    def run_command(flags)
-      file = Tempfile.new("rna")
-      file.write("%s\n" % data.seq)
-      file.write("%s\n" % data.safe_structure)
-      file.close
-      
-      "./FFTbor %s" % file.path
-    end
-    
+  class Fftbor < Xbor
     def partition
-      # Scaling factor (Z{1, n}): 586.684
       response.split(/\n/).find { |line| line =~ /^Scaling factor.*:\s+(\d+\.\d+)/ }
-      $1.to_f
+      BigDecimal.new($1)
     end
     
     def total_count
@@ -23,11 +14,7 @@ module ViennaRna
     end
     
     def distribution
-      self.class.parse(response).map { |row| row[1].to_f }
-    end
-    
-    def self.parse(response)
-      response.split(/\n/).select { |line| line =~ /^\d+\t\d+(\.\d+)?/ }.map { |line| line.split(/\t/) }
+      self.class.parse(response).map { |row| BigDecimal.new(row[1]) }
     end
   end
 end

data/lib/modules/rnabor.rb

@@ -1,16 +1,8 @@
 require "tempfile"
+require "bigdecimal"
 
 module ViennaRna
-  class Rnabor < Base
-    def run_command(flags)
-      file = Tempfile.new("rna")
-      file.write("%s\n" % data.seq)
-      file.write("%s\n" % data.safe_structure)
-      file.close
-      
-      "./RNAbor -nodangle %s" % file.path
-    end
-    
+  class Rnabor < Xbor
     def partition
       non_zero_shells.sum
     end
@@ -23,16 +15,15 @@ module ViennaRna
       (non_zero_counts = self.class.parse(response).map { |row| row[2].to_i }) + [0] * (data.seq.length - non_zero_counts.length + 1)
     end
     
-    def distribution
-      (non_zero_distribution = non_zero_shells.map { |i| i / partition }) + [0.0] * (data.seq.length - non_zero_distribution.length + 1)
+    def distribution(options = {})
+      options = { precision: 4 }.merge(options)
+      
+      distribution_before_precision = (non_zero_distribution = non_zero_shells.map { |i| i / partition }) + [0.0] * (data.seq.length - non_zero_distribution.length + 1)
+      distribution_before_precision.map { |value| options[:precision].zero? ? value : (value * 10 ** options[:precision]).truncate / 10.0 ** options[:precision] }
     end
     
     def non_zero_shells
-      self.class.parse(response).map { |row| row[1].to_f }
-    end
-    
-    def self.parse(response)
-      response.split(/\n/)[2..-1].map { |line| line.split(/\t/) }
+      self.class.parse(response).map { |row| BigDecimal.new(row[1]) }
     end
   end
 end

data/lib/modules/xbor.rb

@@ -0,0 +1,21 @@
+require "tempfile"
+require "bigdecimal"
+
+module ViennaRna
+  class Xbor < Base
+    self.executable_name = -> { name.demodulize.gsub(/^([A-Z].*)bor$/) { |match| $1.upcase + "bor" } }
+    
+    def run_command(flags)
+      file = Tempfile.new("rna")
+      file.write("%s\n" % data.seq)
+      file.write("%s\n" % data.safe_structure)
+      file.close
+      
+      "./%s -nodangle %s" % [exec_name, file.path]
+    end
+    
+    def self.parse(response)
+      response.split(/\n/).select { |line| line =~ /^\d+\t\d+/ }.map { |line| line.split(/\t/) }
+    end
+  end
+end

data/lib/vienna_rna.rb

@@ -3,11 +3,6 @@ require "active_support/inflector"
 require "active_support/core_ext/class"
 require "active_support/core_ext/module/aliasing"
 
-# Clean up this include order.
-Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
-  require file
-end
-
 module Enumerable
   def sum
     inject(&:+)
@@ -17,6 +12,10 @@ end
 module ViennaRna
   @debug = true
   
+  Dir[File.join(File.dirname(__FILE__), "/modules/*")].each do |file|
+    autoload File.basename(file, ".rb").camelize.to_sym, file
+  end
+  
   def self.const_missing(name)
     if Base.exec_exists?(name)
       module_eval do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-21 00:00:00.000000000 Z
+date: 2012-06-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -51,13 +51,13 @@ extra_rdoc_files: []
 files:
 - ./lib/modules/base.rb
 - ./lib/modules/batch.rb
-- ./lib/modules/fft_in_r.rb
 - ./lib/modules/fftbor.rb
 - ./lib/modules/fold.rb
 - ./lib/modules/heat.rb
 - ./lib/modules/rnabor.rb
 - ./lib/modules/subopt.rb
 - ./lib/modules/utils.rb
+- ./lib/modules/xbor.rb
 - ./lib/vienna_rna.rb
 homepage: http://rubygems.org/gems/vienna_rna
 licenses: []

data/lib/modules/fft_in_r.rb

@@ -1,26 +0,0 @@
-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