vienna_rna 0.11.0 → 0.13.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8bc9776db2ef5845bd44177de91c170f00941ce8
-  data.tar.gz: 99c917ee065b84b812f0e32358475f08c5e22880
+  metadata.gz: 099ebe746d12378a62249b9a704ad6774f81e517
+  data.tar.gz: bb38709cf960d5502eaecc608dc848acfdd10abf
 SHA512:
-  metadata.gz: 8bcb4350ac15e7bd7c583adf2bcc81178856a4aa246124359f5fdf74dd6a3603dc182ec66a30f7be351da89363212cf99574f9b512e955c178532da1d2b16c6b
-  data.tar.gz: 8f6b4f63ca2d9f8c41bdc212f35b7be261cfb058631462040fb73cc10fe78d752f122dad28b603c87e256d83509d05a9fc7d0c0787f17502cdf1cb7feb87925f
+  metadata.gz: ae8e3aa5cc99791d32f736a3bc20ef38a0e8a71aa79c96748bd1ceab68a8921e0d3df2519c65c3fd8028e4a3f4866aa001ee7f3a24de3046ac77440e8e8d4945
+  data.tar.gz: 5c35acf8d8ab2d1563c61c7ded6b1dfc155dce50d3e63818a01cebd4abe05eb8b7d3d10432f0ae3edf13d2bce04ebbe097ef2e57f862b2b2970b8ea4780628cd

data/lib/vienna_rna/global/parser.rb

@@ -2,7 +2,8 @@ module ViennaRna
   module Global
     module Parser
       REGEXP = {
-        mfe: / \(\s*(-?\d*\.\d*)\)$/
+        number: /-?\d*\.\d*/,
+        mfe:    / \(\s*(-?\d*\.\d*)\)$/
       }
     
       class << self
@@ -13,6 +14,10 @@ module ViennaRna
         def rnafold_mfe(response)
           response.split(/\n/)[1].match(REGEXP[:mfe])[1].to_f
         end
+        
+        def rnafold_ensemble_energy(response)
+          response.split(/\n/)[2].split(/\s/).last.match(REGEXP[:number])[0].to_f
+        end
       end
     end
   end

data/lib/vienna_rna/global/rna.rb

@@ -4,14 +4,15 @@ module ViennaRna
       include RnaExtensions
     
       attr_accessor :comment
-      attr_reader :sequence, :structure, :second_structure, :raw_data
+      attr_reader :sequence, :structure, :second_structure
       
       class << self
-        def init_from_string(sequence, structure = nil, second_structure = nil)
+        def init_from_string(sequence, structure = nil, second_structure = nil, comment = nil)
           new(
             sequence:         sequence, 
             structure:        structure, 
-            second_structure: second_structure
+            second_structure: second_structure,
+            comment:          comment
           )
         end
     
@@ -20,8 +21,7 @@ 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
+            comment:          hash[:comment]          || hash[:name]
           )
         end
       
@@ -50,16 +50,15 @@ module ViennaRna
             sequence:         rna.sequence, 
             strucutre:        rna.structure, 
             second_strucutre: rna.second_structure, 
-            comment:          rna.comment, 
-            raw_data:         rna.raw_data
+            comment:          rna.comment
           )
         end
       
         alias_method :placeholder, :new
       end
     
-      def initialize(sequence: "", structure: "", second_structure: "", comment: "", raw_data: {})
-        @sequence, @comment, @raw_data = sequence.kind_of?(Rna) ? sequence.seq : sequence, comment, raw_data
+      def initialize(sequence: "", structure: "", second_structure: "", comment: "")
+        @sequence, @comment = sequence.kind_of?(Rna) ? sequence.seq : sequence, comment
       
         [:structure, :second_structure].each do |structure_symbol|
           instance_variable_set(
@@ -96,8 +95,20 @@ module ViennaRna
       def empty_structure
         "." * seq.length
       end
-
+      
       alias :empty_str :empty_structure
+      
+      def one_structure(structure_1)
+        self.class.init_from_string(seq, structure_1.is_a?(Symbol) ? send(structure_1) : structure_1, nil, name)
+      end
+      
+      def two_structures(structure_1, structure_2)
+        self.class.init_from_string(
+          seq, 
+          *[structure_1, structure_2].map { |argument| argument.is_a?(Symbol) ? send(argument) : argument },
+          name
+        )
+      end
     
       def write_fa!(filename)
         filename.tap do |filename|
@@ -117,6 +128,12 @@ module ViennaRna
       def run(package_name, options = {})
         ViennaRna::Package.lookup(package_name).run(self, options)
       end
+      
+      def method_missing(name, *args, &block)
+        if (name_str = "#{name}") =~ /^run_\w+$/
+          run(name_str.gsub(/^run_/, ""), *args)
+        else super end
+      end
 
       def inspect
         "#<RNA: %s>" % [

data/lib/vienna_rna/global/rna_extensions.rb

@@ -43,6 +43,10 @@ module ViennaRna
         def gc_content
           seq.split(//).select { |i| i =~ /[GC]/i }.size.to_f / seq.size
         end
+        
+        def boltzmann_probability(dangle: 2)
+          Math.exp(-run(:eval, d: dangle).mfe / ViennaRna::RT) / Math.exp(-run(:fold, d: dangle, p: 0).ensemble_energy / ViennaRna::RT)
+        end
       end
     
       module OneStructureBasedMethods

data/lib/vienna_rna/global/run_extensions.rb

@@ -19,7 +19,7 @@ module ViennaRna
       
       module InstanceMethods
         def run(flags = {})
-          unless @response
+          unless response
             tap do
               @runtime = Benchmark.measure do
                 pre_run_check
@@ -77,7 +77,9 @@ module ViennaRna
     
         def stringify_flags(flags)
           flags.inject("") do |string, (flag, value)| 
-            (string + (value == :empty ? " -%s" % flag : " -%s %s" % [flag, value])).strip
+            (string + (value == :empty || value.class == TrueClass ? " -%s" % flag : " -%s %s" % [flag, value])).strip
+          end.tap do
+            @flags = flags
           end
         end
       end

data/lib/vienna_rna/graphing/r.rb

@@ -47,9 +47,9 @@ module ViennaRna
             
             r.eval <<-STR
               title(
-                xlab     = "#{x_label}", 
-                ylab     = "#{y_label}", 
-                main     = "#{title || 'Line Graph'}",
+                xlab     = #{expressionify(x_label)}, 
+                ylab     = #{expressionify(y_label)}, 
+                main     = #{expressionify(title || "Line Graph")},
                 cex.main = .9,
                 cex.lab  = .9
               )
@@ -60,11 +60,12 @@ module ViennaRna
                 legend(
                   "#{legend}",
                   legend.titles,
-                  bty = "n",
+                  bty = "o",
+                  bg  = rgb(1, 1, 1, .5, 1),
                   col = line.colors,
                   lty = rep(1, #{data.size}),
                   pch = 0:#{data.size},
-                  cex = .9
+                  cex = .6
                 )
               STR
             end
@@ -78,7 +79,7 @@ module ViennaRna
         end
         
         def scatterplot(data, title: nil, x_label: "Independent", y_label: "Dependent", filename: false)
-          line_graph(data, title: title, type: ?p, x_label: x_label, y_label: y_label, filename: filename)
+          line_graph(data, title: title || "Scatterplot", type: ?p, x_label: x_label, y_label: y_label, filename: filename)
         end
         
         def roc(data, title: nil, baseline: true, filename: false)
@@ -139,8 +140,8 @@ module ViennaRna
               hist(
                 histogram.data, 
                 breaks   = histogram.breaks, 
-                xlab     = "#{x_label}", 
-                main     = "#{title || 'Histogram'}", 
+                xlab     = #{expressionify(x_label)}, 
+                main     = #{expressionify(title || "Histogram")}, 
                 freq     = #{relative ? 'F' : 'T'},
                 cex.main = 0.9,
                 cex.lab  = 0.9,
@@ -191,7 +192,7 @@ module ViennaRna
                     xlab = "#{x_label} (1-indexed)",
                     ylab = "#{y_label} (1-indexed)"
                   )
-                  title("#{title || 'Matrix Heatmap'}")
+                  title(#{expressionify(title || "Matrix Heatmap")})
                 STR
               end
             else
@@ -218,6 +219,10 @@ module ViennaRna
         def writing_file?(filename)
           filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
         end
+        
+        def expressionify(string)
+          %w|expression paste|.any?(&string.method(:start_with?)) ? string : string.inspect
+        end
       end
     end
   end

data/lib/vienna_rna/package/base.rb

@@ -24,11 +24,12 @@ module ViennaRna
         def bootstrap(data: nil, output: "")
           new(data).tap do |object|
             object.instance_variable_set(:@response, File.exist?(output) ? File.read(output).chomp : output)
+            object.post_process if object.respond_to?(:post_process)
           end
         end
       end
     
-      attr_reader :data, :response, :runtime
+      attr_reader :data, :flags, :response, :runtime
     
       def initialize(data, chaining: false)
         unless chaining
@@ -54,6 +55,16 @@ module ViennaRna
       def debugger(&block)
         self.class.debugger(&block)
       end
+      
+      def inspect
+        "#<%s (%.2f sec): data: %s, flags: %s, vars: %s>" % [
+          self.class.name,
+          runtime.real,
+          data,
+          flags,
+          (instance_variables - %i|@data @flags @response @runtime|).map(&:to_s).sort.join(", ")
+        ]
+      end
     end
   end
 end

data/lib/vienna_rna/package/eval.rb

@@ -6,7 +6,7 @@ module ViennaRna
       attr_reader :mfe
     
       def post_process
-        @mfe = ViennaRna::Global::Parser.rnafold_mfe(@response)
+        @mfe = ViennaRna::Global::Parser.rnafold_mfe(response)
       end
     end
   end

data/lib/vienna_rna/package/fft_mfpt.rb

@@ -0,0 +1,24 @@
+# Maybe add something like flagsets so that common option groups can be combined together.
+# Also, add a rerun feature.
+
+module ViennaRna
+  module Package
+    class FftMfpt < Base
+      self.executable_name = "FFTmfpt"
+      
+      attr_reader :mfpt
+    
+      def run_command(flags)      
+        "%s %s %s" % [
+          exec_name, 
+          stringify_flags(flags), 
+          data.temp_fa_file!
+        ]
+      end
+    
+      def post_process
+        @mfpt = response.to_f
+      end
+    end
+  end
+end

data/lib/vienna_rna/package/fftbor2d.rb

@@ -2,7 +2,24 @@ module ViennaRna
   module Package
     class Fftbor2d < EnergyGrid2d
       self.executable_name = "FFTbor2D"
-      self.default_flags   = ->(_, flags) { (flags.keys & %i|X M S|).empty? ? { S: :empty } : {} }
+      self.default_flags   = ->(_, flags) { (flags.keys & %i|X Y M S|).empty? ? { S: :empty } : {} }
+      
+      attr_reader :population_proportion_str_2_from_str_1, :population_proportion_for_str_1
+      
+      class Population
+        attr_reader :proportion_over_time
+  
+        def initialize(time, proportion)
+          @proportion_over_time = time.zip(proportion)
+        end
+        
+        def time_range(from, to)
+          proportion_over_time.select { |time, _| ((from.to_f)..(to.to_f)) === time }
+        end
+        
+        def time_points; proportion_over_time.map(&:first); end
+        def proportion_points; proportion_over_time.map(&:last); end
+      end
 
       def run_command(flags)
         ViennaRna.debugger { "Running #{exec_name} on #{data.inspect}" }
@@ -13,6 +30,14 @@ module ViennaRna
           data.temp_fa_file!
         ]
       end
+      
+      def post_process
+        if flags.keys.include?(:Y)
+          time_points, proportion_str_2_from_str_1, proportion_for_str_1 = response.split(/\n/).map { |line| line.split(/\t/).map(&:to_f) }.transpose
+          @population_proportion_str_2_from_str_1                        = Population.new(time_points, proportion_str_2_from_str_1)
+          @population_proportion_for_str_1                               = Population.new(time_points, proportion_for_str_1)
+        end
+      end
     
       def distribution
         response.split(/\n/).map { |line| line.split(/\t/) }

data/lib/vienna_rna/package/fold.rb

@@ -5,15 +5,19 @@ module ViennaRna
         "-noPS" => :empty
       }
     
-      attr_reader :mfe_rna, :structure, :mfe
+      attr_reader :mfe_rna, :structure, :mfe, :ensemble_energy
     
       def post_process
-        structure = ViennaRna::Global::Parser.rnafold_mfe_structure(@response)
+        structure = ViennaRna::Global::Parser.rnafold_mfe_structure(response)
       
         unless data.seq.length == structure.length
           raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
         else
-          @mfe_rna, @structure, @mfe = RNA.from_string(data.seq, structure), structure, ViennaRna::Global::Parser.rnafold_mfe(@response)
+          @mfe_rna, @structure, @mfe = RNA.from_string(data.seq, structure), structure, ViennaRna::Global::Parser.rnafold_mfe(response)
+        end
+        
+        if flags[:p] == 0
+          @ensemble_energy = ViennaRna::Global::Parser.rnafold_ensemble_energy(response)
         end
       end
     end

data/lib/vienna_rna/package/heat.rb

@@ -4,7 +4,7 @@ module ViennaRna
       attr_reader :specific_heats
     
       def post_process
-        @specific_heats = @response.split(/\n/).map { |line| line.split(/\s+/).map(&:to_f) }.inject({}) do |hash, (temp, specific_heat)|
+        @specific_heats = response.split(/\n/).map { |line| line.split(/\s+/).map(&:to_f) }.inject({}) do |hash, (temp, specific_heat)|
           hash.tap do
             hash[temp] = specific_heat
           end

data/lib/vienna_rna/package/kinwalker.rb

@@ -0,0 +1,24 @@
+module ViennaRna
+  module Package
+    class Kinwalker < Base
+      self.executable_name = "kinwalker"
+      attr_reader :nodes
+                
+      def post_process
+        @nodes = response.split("TRAJECTORY").last.split(?\n).reject(&:empty?)[0..-2].map { |line| Node.new(*line.split(/\s+/)) }
+      end
+      
+      def mfpt
+        nodes.last.time
+      end
+      
+      class Node
+        attr_reader :structure, :energy, :time, :barrier, :energy_barrier, :transcribed
+        
+        def initialize(structure, energy, time, barrier, energy_barrier, transcribed)
+          @structure, @energy, @time, @barrier, @energy_barrier, @transcribed = structure, energy.to_f, time.to_f, barrier.to_f, energy_barrier.to_f, transcribed.to_i
+        end
+      end
+    end
+  end
+end

data/lib/vienna_rna/package/mfpt.rb

@@ -1,4 +1,5 @@
 # Maybe add something like flagsets so that common option groups can be combined together.
+# Also, add a rerun feature.
 
 module ViennaRna
   module Package
@@ -32,8 +33,8 @@ module ViennaRna
       end
     
       def post_process
-        @mfpt = @response.to_f
+        @mfpt = response.to_f
       end
     end
   end
-end
+end

data/lib/vienna_rna/package/rna2dfold.rb

@@ -3,8 +3,8 @@ module ViennaRna
     class Rna2dfold < EnergyGrid2d
       self.default_flags = {
         d:         0,
-        p:         :empty,
-        "-noBT" => :empty
+        p:         true,
+        "-noBT" => true
       }
 
       self.executable_name = "RNA2Dfold"

data/lib/vienna_rna/package/spectral.rb

@@ -0,0 +1,24 @@
+module ViennaRna
+  module Package
+    class Spectral < Base      
+      self.default_flags = ->(context, flags) { { seq: context.data.seq, step_size: "1e-2" } }
+      
+      attr_reader :eigenvalues, :time_kinetics
+    
+      def run_command(flags)
+        "%s %s" % [
+          exec_name, 
+          stringify_flags(flags)
+        ]
+      end
+    
+      def post_process
+        if flags.keys.include?(:eigen_only)
+          @eigenvalues = response.split(?\n).map(&:to_f).sort_by(&:abs)
+        else
+          @time_kinetics = response.split(?\n).map { |line| line.split(?\t).map(&:to_f) }
+        end
+      end
+    end
+  end
+end

data/lib/vienna_rna/package/subopt.rb

@@ -4,7 +4,7 @@ module ViennaRna
       attr_reader :structures
     
       def post_process
-        @structures = @response.split(/\n/)[1..-1].map { |output| RNA.from_string(data.seq, output.split(/\s+/).first) }
+        @structures = response.split(/\n/)[1..-1].map { |output| RNA.from_string(data.seq, output.split(/\s+/).first) }
       end
     
       def bin(count = 1)

data/lib/vienna_rna/package/tabu_path.rb

@@ -21,7 +21,7 @@ module ViennaRna
       end
     
       def post_process
-        @paths = @response.split(data.str_1 + ?\n).reject(&:empty?).map { |path_string| Path.new(data, path_string) }
+        @paths = response.split(data.str_1 + ?\n).reject(&:empty?).map { |path_string| Path.new(data, path_string) }
       end
       
       class Path
@@ -40,6 +40,10 @@ module ViennaRna
         def full_path?
           rna.str_1 == path.first && rna.str_2 == path.last
         end
+        
+        def inspect
+          "#<#{self.class.name} with barrier %.2f and length %d on #{rna.inspect}>" % [barrier, best_weight]
+        end
       end
     end
   end

data/lib/vienna_rna/package/xbor.rb

@@ -2,7 +2,7 @@ module ViennaRna
   module Package
     class Xbor < Base
       self.default_flags = {
-        E: "/usr/local/bin/energy.par"
+        E: "/usr/local/bin/rna_turner2004.par"
       }
     
       self.executable_name = ->(context) { context.class.name.demodulize.gsub(/^([A-Z].*)bor$/) { |match| $1.upcase + "bor" } }
@@ -22,14 +22,6 @@ module ViennaRna
         ]
       end
     
-      def self.bootstrap_from_file(path, klass = self)
-        log       = File.read(path)
-        sequence  = log.split(/\n/).first.split(/\s+/)[1]
-        structure = log.split(/\n/).first.split(/\s+/)[2]
-      
-        klass.bootstrap(data: RNA.from_string(sequence, structure), output: log)
-      end
-    
       def self.parse(response)
         response.split(/\n/).select { |line| line =~ /^\d+\t-?\d+/ }.map { |line| line.split(/\t/) }
       end
@@ -46,12 +38,20 @@ module ViennaRna
       def expected_k
         k_p_points.map { |array| array.inject(&:*) }.inject(&:+)
       end
+      
+      def to_csv
+        k_p_points.map { |k, p| "%d,%.8f" % [k, p] }.join(?\n) + ?\n
+      end
+      
+      def to_csv!(filename)
+        File.open(filename, ?w) { |file| file.write(to_csv) }
+      end
     
-      def quick_plot(options = {})
-        ViennaRna::Graphing::Gnuplot.quick_plot(
+      def quick_plot(filename: false)
+        ViennaRna::Graphing::R.line_graph(
           k_p_points,
-          options[:title] || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure],
-          options
+          title:    options[:title] || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure],
+          filename: false
         )
       end
     

data/lib/vienna_rna.rb

@@ -63,6 +63,10 @@ unless defined? RNA
 end
 
 module RNA
+  def self.load_all(pattern: "*.fa")
+    Dir[pattern].map { |file| RNA.from_fasta(file) }
+  end
+  
   def self.random(size, *args)
     RNA.from_array(args.unshift(ViennaRna::Global::Rna.generate_sequence(size).seq))
   end

metadata

@@ -1,33 +1,36 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.11.0
+  version: 0.13.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-25 00:00:00.000000000 Z
+date: 2014-02-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.2'
 - !ruby/object:Gem::Dependency
   name: shuffle
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.0
@@ -35,6 +38,9 @@ dependencies:
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.0
@@ -42,6 +48,9 @@ dependencies:
   name: rinruby
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
@@ -49,6 +58,9 @@ dependencies:
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.0.3
@@ -56,6 +68,9 @@ dependencies:
   name: rroc
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.1
@@ -63,6 +78,9 @@ dependencies:
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.1
@@ -73,6 +91,8 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- README.md
+- lib/vienna_rna.rb
 - lib/vienna_rna/global/chain_extensions.rb
 - lib/vienna_rna/global/parser.rb
 - lib/vienna_rna/global/rna.rb
@@ -82,20 +102,21 @@ files:
 - lib/vienna_rna/package/base.rb
 - lib/vienna_rna/package/energy_grid_2d.rb
 - lib/vienna_rna/package/eval.rb
+- lib/vienna_rna/package/fft_mfpt.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/kinwalker.rb
 - lib/vienna_rna/package/mfpt.rb
 - lib/vienna_rna/package/rna2dfold.rb
 - lib/vienna_rna/package/rnabor.rb
+- lib/vienna_rna/package/spectral.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
 homepage: http://rubygems.org/gems/vienna_rna
 licenses: []
 metadata: {}
@@ -115,7 +136,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.11
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
 summary: Bindings to the Vienna RNA package, and other major command line utilities