vienna_rna 0.10.0 → 0.11.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 99c917ee065b84b812f0e32358475f08c5e22880
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data/lib/vienna_rna.rb

@@ -4,7 +4,7 @@ require "shuffle"
 require "rinruby"
 require "tempfile"
 require "bigdecimal"
-require "diverge"
+require "rroc"
 require "active_support/inflector"
 require "active_support/core_ext/class"
 
@@ -63,6 +63,10 @@ unless defined? RNA
 end
 
 module RNA
+  def self.random(size, *args)
+    RNA.from_array(args.unshift(ViennaRna::Global::Rna.generate_sequence(size).seq))
+  end
+  
   def self.method_missing(name, *args, &block)
     if "#{name}" =~ /^from_\w+$/
       ViennaRna::Global::Rna.send("init_#{name}", *args)

data/lib/vienna_rna/global/chain_extensions.rb

@@ -17,7 +17,7 @@ module ViennaRna
             raise ArgumentError.new("#{class_chaining_to.name} doesn't support chaining because it doesn't define transform_for_chaining")
           end
           
-          unless [chains_from].flatten.any? { |chaining_from| kind_of?(chaining_from) }
+          unless [chains_from].flatten.any?(&method(:kind_of?))
             raise ArgumentError.new("#{class_chaining_to.name} doesn't support chaining from #{self.class.name} because it isn't in the chains_from list")
           end
           

data/lib/vienna_rna/global/rna.rb

@@ -3,6 +3,7 @@ module ViennaRna
     class Rna
       include RnaExtensions
     
+      attr_accessor :comment
       attr_reader :sequence, :structure, :second_structure, :raw_data
       
       class << self
@@ -19,6 +20,7 @@ module ViennaRna
             sequence:         hash[:sequence]         || hash[:seq], 
             structure:        hash[:structure]        || hash[:str_1] || hash[:str], 
             second_structure: hash[:second_structure] || hash[:str_2], 
+            comment:          hash[:comment]          || hash[:name], 
             raw_data:         hash
           )
         end
@@ -28,8 +30,18 @@ module ViennaRna
         end
       
         def init_from_fasta(string)
-          string = File.read(string).chomp if File.exist?(string)
-          init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") }[0, 3])
+          if File.exist?(string)
+            comment = File.basename(string, string.include?(?.) ? ".%s" % string.split(?.)[-1] : "")
+            string  = File.read(string).chomp
+          end
+          
+          init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") }[0, 3]).tap do |rna|
+            if (line = string.split(/\n/).first).start_with?(">") && !(file_comment = line.gsub(/^>\s*/, "")).empty?
+              rna.comment = file_comment
+            elsif comment
+              rna.comment = comment
+            end
+          end
         end
     
         def init_from_self(rna)
@@ -38,6 +50,7 @@ module ViennaRna
             sequence:         rna.sequence, 
             strucutre:        rna.structure, 
             second_strucutre: rna.second_structure, 
+            comment:          rna.comment, 
             raw_data:         rna.raw_data
           )
         end
@@ -45,8 +58,8 @@ module ViennaRna
         alias_method :placeholder, :new
       end
     
-      def initialize(sequence: "", structure: "", second_structure: "", raw_data: {})
-        @sequence, @raw_data = sequence.kind_of?(Rna) ? sequence.seq : sequence, raw_data
+      def initialize(sequence: "", structure: "", second_structure: "", comment: "", raw_data: {})
+        @sequence, @comment, @raw_data = sequence.kind_of?(Rna) ? sequence.seq : sequence, comment, raw_data
       
         [:structure, :second_structure].each do |structure_symbol|
           instance_variable_set(
@@ -78,6 +91,7 @@ module ViennaRna
       alias :str   :structure
       alias :str_1 :structure
       alias :str_2 :second_structure
+      alias :name  :comment
     
       def empty_structure
         "." * seq.length
@@ -85,13 +99,13 @@ module ViennaRna
 
       alias :empty_str :empty_structure
     
-      def write_fa!(filename, comment = nil)
+      def write_fa!(filename)
         filename.tap do |filename|
           File.open(filename, ?w) do |file|
-            file.write("> %s\n" % comment) if comment
-            file.write("%s\n" % seq)       if seq
-            file.write("%s\n" % str_1)     if str_1
-            file.write("%s\n" % str_2)     if str_2
+            file.write("> %s\n" % name) if name
+            file.write("%s\n" % seq)    if seq
+            file.write("%s\n" % str_1)  if str_1
+            file.write("%s\n" % str_2)  if str_2
           end
         end
       end
@@ -105,12 +119,12 @@ module ViennaRna
       end
 
       def inspect
-        "#<%s>" % [
-          "#{self.class.name}",
-          ("#{seq[0, 20]   + (seq.length > 20   ? '...' : '')}"          if seq && !seq.empty?),
-          ("#{str_1[0, 20] + (str_1.length > 20 ? ' [truncated]' : '')}" if str_1 && !str_1.empty?),
-          ("#{str_2[0, 20] + (str_2.length > 20 ? ' [truncated]' : '')}" if str_2 && !str_1.empty?),
-        ].compact.join(" ")
+        "#<RNA: %s>" % [
+          ("#{seq[0, 20]   + (seq.length > 20   ? '... [%d]' % seq.length : '')}" if seq   && !seq.empty?),
+          ("#{str_1[0, 20] + (str_1.length > 20 ? ' [%d]'    % seq.length : '')}" if str_1 && !str_1.empty?),
+          ("#{str_2[0, 20] + (str_2.length > 20 ? ' [%d]'    % seq.length : '')}" if str_2 && !str_1.empty?),
+          (!name.empty? ? name : "#{self.class.name}")
+        ].compact.join(", ")
       end
     end
   end

data/lib/vienna_rna/global/run_extensions.rb

@@ -8,7 +8,7 @@ module ViennaRna
       
       module ClassMethods
         def exec_exists?(name)
-          !%x[which RNA#{name.to_s.downcase}].empty?
+          !%x[which RNA#{name.to_s.downcase}].empty? || !%x[which #{name.to_s.downcase}].empty?
         end
         
         def run(*data)

data/lib/vienna_rna/graphing/r.rb

@@ -81,6 +81,46 @@ module ViennaRna
           line_graph(data, title: title, type: ?p, x_label: x_label, y_label: y_label, filename: filename)
         end
         
+        def roc(data, title: nil, baseline: true, filename: false)
+          # data: [[-0.894, 1.0], [-0.950, 1.0], [0.516, -1.0], ..., [0.815, -1.0], [0.740, -1.0]]
+          auc            = ROC.auc(data)
+          title_with_auc = title ? "%s (AUC: %.4f)" % [title, auc] : "AUC: %.4f" % auc
+          overlay(
+            [{ data: ROC.curve_points(data) }, { data: [[0, 0], [1, 1]] }], 
+            title:    title_with_auc, 
+            x_label:  "False positive rate", 
+            y_label:  "True positive rate", 
+            legend:   false, 
+            filename: filename
+          )
+        end
+        
+        def roc_overlay(data, title: nil, auc_in_legend: true, filename: false)
+          # [{ data: [[-0.894, 1.0], [-0.950, 1.0], [0.516, -1.0], ..., [0.815, -1.0], [0.740, -1.0]], legend: "ROC 1" }, ...]
+          formatted_data = data.map do |hash|
+            curve_points = ROC.curve_points(hash[:data])
+            
+            if auc_in_legend
+              auc    = ROC.auc(hash[:data])
+              legend = hash[:legend] ? "%s (AUC: %.4f)" % [hash[:legend], auc] : "AUC: %.4f" % auc
+              
+              hash.merge({ data: curve_points, legend: legend })
+            else
+              hash.merge({ data: curve_points })
+            end
+          end
+          
+          
+          overlay(
+            formatted_data, 
+            title:    title, 
+            x_label:  "False positive rate", 
+            y_label:  "True positive rate", 
+            legend:   "bottomright", 
+            filename: filename
+          )
+        end
+        
         def histogram(data, title: nil, x_label: "Bins", num_bins: false, bin_size: 1, x_arrow: false, relative: false, filename: false)
           half     = bin_size / 2.0
           range    = Range.new((data.min - half).floor, (data.max + half).ceil)
@@ -160,27 +200,6 @@ module ViennaRna
           end
         end
         
-        def roc(data, title = "", options = {})
-          # data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]
-
-          if R.pull("ifelse('ROCR' %in% rownames(installed.packages()), 1, -1)") > 0
-
-          else
-            puts "Please install the ROCR package for R before using this function."
-          end
-
-          # 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]
-          #   sum + (delta_x * delta_y / 2 + delta_x * [a[1], b[1]].min)
-          # end
-          
-          # options.merge!(output: "file") if options[:filename]
-          # options.merge!({ plot: { title: "%s %s %.4f" % [title, "AUC:", area] } })
-    
-          # plot([{ x: roc_curve.map(&:first), y: roc_curve.map(&:last), style: "lines" }], options)
-        end
-        
         private
         
         def generate_graph(window_title = "ViennaRNA Graph in R", &block)

data/lib/vienna_rna/package/ffthairpin.rb

@@ -0,0 +1,7 @@
+module ViennaRna
+  module Package
+    class Ffthairpin < Fftbor
+      self.executable_name = "FFThairpin"
+    end
+  end
+end

data/lib/vienna_rna/package/fftmultiloop.rb

@@ -0,0 +1,7 @@
+module ViennaRna
+  module Package
+    class Fftmultiloop < Fftbor
+      self.executable_name = "FFTmultiloop"
+    end
+  end
+end

data/lib/vienna_rna/package/mfpt.rb

@@ -1,8 +1,10 @@
+# Maybe add something like flagsets so that common option groups can be combined together.
+
 module ViennaRna
   module Package
     class Mfpt < Base
       self.chains_from   = ViennaRna::Package::EnergyGrid2d
-      self.default_flags = ->(context, flags) { { X: :empty, H: :empty, N: context.data.seq.length, Q: "1e-8" } }
+      self.default_flags = ->(context, flags) { { X: :empty, H: :empty, N: context.data.seq.length, D: context.data.bp_distance, Q: "1e-8" } }
       # These flags aren't well setup for alternative options at the moment.
       
       attr_reader :mfpt
@@ -10,11 +12,13 @@ module ViennaRna
       def transform_for_chaining(previous_package)
         previous_package.data.tap do |data|
           data.instance_eval do
-            @energy_grid_csv = Tempfile.new("rna").path.tap do |energy_grid_csv|
-              previous_package.to_csv!(energy_grid_csv)
+            @previous_package = previous_package
+            
+            def energy_grid_csv
+              Tempfile.new("rna").path.tap do |energy_grid_csv|
+                @previous_package.to_csv!(energy_grid_csv)
+              end
             end
-          
-            def energy_grid_csv; @energy_grid_csv; end
           end
         end
       end

data/lib/vienna_rna/package/tabu_path.rb

@@ -0,0 +1,46 @@
+module ViennaRna
+  module Package
+    class TabuPath < Base
+      self.executable_name = "get_barrier_tabu"
+      self.default_flags   = ->(context, flags) { { iterations: 10, min_weight: 10, max_weight: 70 } }
+      
+      attr_reader :paths
+    
+      def run_command(flags)
+        ViennaRna.debugger { "Running #{exec_name} on #{data.inspect}" }
+      
+        [
+          exec_name, 
+          data.seq.inspect,
+          data.str_1.inspect,
+          data.str_2.inspect,
+          flags[:iterations],
+          flags[:min_weight],
+          flags[:max_weight]
+        ].join(" ")
+      end
+    
+      def post_process
+        @paths = @response.split(data.str_1 + ?\n).reject(&:empty?).map { |path_string| Path.new(data, path_string) }
+      end
+      
+      class Path
+        attr_reader :rna, :path, :barrier, :best_weight
+        
+        def initialize(rna, output)
+          @rna                      = rna
+          @path                     = output.split(?\n)[0..-2].unshift(rna.str_1)
+          @barrier, _, @best_weight = output.split(?\n)[-1].gsub(/[^\d\.]/, " ").strip.split(/\s+/).map(&:to_f)
+        end
+        
+        def length
+          path.length
+        end
+        
+        def full_path?
+          rna.str_1 == path.first && rna.str_2 == path.last
+        end
+      end
+    end
+  end
+end

data/lib/vienna_rna/package/xbor.rb

@@ -27,7 +27,7 @@ module ViennaRna
         sequence  = log.split(/\n/).first.split(/\s+/)[1]
         structure = log.split(/\n/).first.split(/\s+/)[2]
       
-        klass.bootstrap(RNA.from_string(sequence, structure), log)
+        klass.bootstrap(data: RNA.from_string(sequence, structure), output: log)
       end
     
       def self.parse(response)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.10.0
+  version: 0.11.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-03 00:00:00.000000000 Z
+date: 2013-11-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -52,6 +52,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
+- !ruby/object:Gem::Dependency
+  name: rroc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.1
 description: A Ruby 2.0 API for interacting with command line tools involving RNA
   molecules through a standard interface.
 email: evansenter@gmail.com
@@ -70,12 +84,15 @@ files:
 - lib/vienna_rna/package/eval.rb
 - lib/vienna_rna/package/fftbor.rb
 - lib/vienna_rna/package/fftbor2d.rb
+- lib/vienna_rna/package/ffthairpin.rb
+- lib/vienna_rna/package/fftmultiloop.rb
 - lib/vienna_rna/package/fold.rb
 - lib/vienna_rna/package/heat.rb
 - lib/vienna_rna/package/mfpt.rb
 - lib/vienna_rna/package/rna2dfold.rb
 - lib/vienna_rna/package/rnabor.rb
 - lib/vienna_rna/package/subopt.rb
+- lib/vienna_rna/package/tabu_path.rb
 - lib/vienna_rna/package/xbor.rb
 - lib/vienna_rna.rb
 - README.md
@@ -98,7 +115,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.9
+rubygems_version: 2.1.11
 signing_key: 
 specification_version: 4
 summary: Bindings to the Vienna RNA package, and other major command line utilities