vienna_rna 0.3.0 → 0.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: f3e2f41a3957ca6a84cd38aaa390ae383a49f712
+  metadata.gz: 125876026dfe4b5bf2af8e12fe1425c79ce2c41f
+  data.tar.gz: 28cff69aaabc513509da57f049928b7d1f62dc82
 SHA512:
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+  data.tar.gz: dce9820a4cd5a0ae1b86b6aa329cff3b6373d5ea9892a156940097e58955f793be3e7ecbd902ab7340cc6db112169151302998805e1278842780ce3e6a3fb6d7

data/lib/vienna_rna/modules/rna.rb

@@ -40,6 +40,7 @@ module ViennaRna
     alias :seq :sequence
     alias :str :structure
     
+    
     def inspect
       case [sequence.present?, structure.present?]
       when [true, true] then
@@ -60,6 +61,10 @@ module ViennaRna
         end
       end
     end
+
+    def run(module_name, options = {})
+      ViennaRna.const_missing("#{module_name}".camelize).run(self, options)
+    end
     
     private
       

data/lib/vienna_rna/modules/rna_extensions.rb

@@ -2,6 +2,7 @@ module ViennaRna
   module RnaExtensions
     def self.included(base)
       base.extend(ClassMethods)
+      base.send(:include, InstanceMethods)
       base.extend(StructureBasedClassAndInstanceMethods)
       
       base.class_eval do
@@ -25,6 +26,12 @@ module ViennaRna
         Shuffle.new(sequence).shuffle(token_length)
       end
     end
+
+    module InstanceMethods
+      def gc_content
+        seq.split(//).select { |i| i =~ /[GC]/i }.size.to_f / seq.size
+      end
+    end
     
     module StructureBasedClassAndInstanceMethods
       # All the methods in here are also copied in as instance methods, where the first argument is the ViennaRna::Rna#structure

data/lib/vienna_rna/modules/utils.rb

@@ -91,23 +91,18 @@ module ViennaRna
         groups   = (range.min + half).step(range.max, bin_size).map { |x| [x, data.count { |i| i >= x - half && i < x + half }] }
         
         options.merge!(output: "file") if options[:filename]
-        options.merge!({
-          plot: {
-            title:  title,
-            yrange: "[0:#{groups.map(&:last).max * 1.1}]",
-            xtics:  "#{[bin_size, 5].max}",
-            style:  "fill solid 0.5 border"
-          }
+        options[:plot] = (options[:plot] || {}).merge({
+          title:  title,
+          yrange: "[0:#{groups.map(&:last).max * 1.1}]",
+          xtics:  "#{[bin_size, 5].max}",
+          style:  "fill solid 0.5 border"
         })
   
         plot([{ x: groups.map(&:first), y: groups.map(&:last), style: "boxes" }], options)
       end
       
       def roc(data, title = "", options = {})
-        # data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]
-        # This 'twiddle' removes duplicates by adding a very small random number to any repeated value
-        data = data.map { |scores| scores.group_by(&:_ident).values.inject([]) { |array, values| array + (values.size > 1 ? values.map { |i| i + 1e-8 * (rand - 0.5) } : values) } }
-        
+        # data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]~
         roc_curve = ROC.curve_points({ 1 => data[0], -1 => data[1] }.inject([]) { |data, (truth, values)| data.concat(values.map { |i| [i, truth] })})
         area      = roc_curve.each_cons(2).inject(0) do |sum, (a, b)| 
           delta_x, delta_y = b[0] - a[0], b[1] - a[1]
@@ -129,7 +124,7 @@ module ViennaRna
         options[:plot] = ((options[:plot] || {}).merge(title: title))
         options.merge!(output: "file") if options[:filename]
         
-        plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[: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" }.merge(hash[:options] || {}) }, options)
       end
     end
   end

data/lib/vienna_rna.rb

@@ -17,7 +17,9 @@ module ViennaRna
   end
   
   def self.const_missing(name)
-    if Base.exec_exists?(name)
+    if const_defined?(name)
+      const_get(name)
+    elsif Base.exec_exists?(name)
       module_eval do
         const_set(name, Class.new(Base))
       end
@@ -31,4 +33,11 @@ module ViennaRna
   def self.debug=(value)
     @debug = value
   end
+end
+
+# This dirties up the public namespace, but I use it so many times that I want a shorthand to it
+unless defined? RNA
+  def RNA(sequence, structure = nil)
+    ViennaRna::Rna.init_from_string(sequence, structure)
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-29 00:00:00.000000000 Z
+date: 2013-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -123,7 +123,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.2
+rubygems_version: 2.0.3
 signing_key: 
 specification_version: 4
 summary: Bindings to the Vienna RNA package.