vienna_rna 0.7.0 → 0.8.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 80d4f6159bca186181c792f0a09d696db387a4e3
-  data.tar.gz: 50bc4db672365259c1c25f78659b268e5d3c60c6
+  metadata.gz: 99cbd2a9afe1fb15daae72432caf558589d780f9
+  data.tar.gz: fbb4a27a788983898147fbb67bcbf91cae0cbaed
 SHA512:
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-  data.tar.gz: c16e11c3a1e79b2b909692b173b90bf2a20568823376d270859fcbd5133ba09d751d409531ae5c8b1d9c4f44d1f6aced99148791ab98b9690cef5dbf511e73ee
+  metadata.gz: 17f72d39b411f7ad5b19aaa60d11e91e392a86eae84712f95c804ce121648f55b85adbb904bf536ec137b590707f70d6b66b4a85cdf501501e0e68b8286f224f
+  data.tar.gz: 550bb20dbbc67f04cec01471db211378aa50e5784296c603f1871e2ab60d3bda6f02e2924d97cba4cbd39ab5d4b268392aa2634a55b1758e089187b3252e7ce1

data/lib/vienna_rna/modules/base.rb

@@ -25,12 +25,13 @@ module ViennaRna
         new(data).run(flags)
       end
       
-      def bootstrap(data, output)
+      def bootstrap(data: nil, output: "")
         new(data).tap do |object|
-          object.instance_variable_set(:@response, output)
+          object.instance_variable_set(:@response, File.exist?(output) ? File.read(output).chomp : output)
         end
       end
       
+      # Time to redo batch stuff.
       def batch(fastas = [])
         ViennaRna::Batch.new(self, fastas).tap do |batch|
           if const_defined?(:Batch)
@@ -69,6 +70,7 @@ module ViennaRna
       when *(1..3).map { |i| [String] * i } then Rna.init_from_string(*data)
       when [Hash]                           then Rna.init_from_hash(*data)
       when [Array]                          then Rna.init_from_array(*data)
+      when [NilClass]                       then Rna.placeholder
       else raise TypeError.new("Unsupported ViennaRna::Rna#initialize format: #{data}")
       end
     end

data/lib/vienna_rna/modules/energy_grid_2d.rb

@@ -0,0 +1,63 @@
+module ViennaRna
+  class EnergyGrid2d < Base
+    include Enumerable
+    
+    def self.inherited(subclass)
+      subclass.class_eval { prepend EnergyGrid2dWrapper }
+    end
+    
+    module EnergyGrid2dWrapper
+      def distribution
+        super.map { |row| Row2d.new(*row) }.select { |row| row.p > 0 }.sort
+      end
+    end
+    
+    class Row2d
+      attr_reader :i, :j, :p, :ensemble
+  
+      def initialize(i, j, p, ensemble)
+        @i, @j, @p, @ensemble = i.to_i, j.to_i, BigDecimal.new(p.to_s), BigDecimal.new(ensemble.to_s)
+      end
+      
+      def position
+        [i, j]
+      end
+    
+      def <=>(other_row)
+        i == other_row.i ? j <=> other_row.j : i <=> other_row.i
+      end
+      
+      def inspect
+        "#<Row2d (%d, %d), p: %+f, ensemble: %+f>" % [i, j, p, ensemble]
+      end
+    end
+    
+    def self.aligned_distributions(*energy_grids)
+      point_set = set_of_points(*energy_grids)
+      
+      energy_grids.map do |grid|
+        (grid.distribution + (point_set - grid.map(&:position)).map { |i, j| Row2d.new(i, j, 0, Float::INFINITY) }).sort
+      end
+    end
+    
+    def self.set_of_points(*energy_grids)
+      energy_grids.inject([]) { |list, grid| list + grid.map(&:position) }.uniq.sort
+    end
+    
+    def each(&block)
+      distribution.each(&block)
+    end
+    
+    def quick_plot(num_colors: 8)
+      Graphing::R.matrix_heatmap(
+        distribution.map(&:i), 
+        distribution.map(&:j), 
+        distribution.map { |row| Math.log(row.p) },
+        title:      "#{self.class.name} Matrix Heatmap",
+        x_label:    "Distance from structure 2",
+        y_label:    "Distance from structure 1",
+        num_colors: num_colors
+      )
+    end
+  end
+end

data/lib/vienna_rna/modules/fftbor2d.rb

@@ -1,8 +1,6 @@
 module ViennaRna
-  class Fftbor2d < Base
+  class Fftbor2d < EnergyGrid2d
     BASE_FLAGS = {
-      E: "/usr/local/bin/rna_turner1999.par",
-      P: 8,
       S: :empty
     }
 
@@ -19,10 +17,7 @@ module ViennaRna
     end
     
     def distribution
-      response.split(/\n/).map do |line| 
-        i, j, p, ensemble = line.split(/\t/)
-        [i, j].map(&:to_i) + [p, ensemble].map(&:to_f)
-      end
+      response.split(/\n/).map { |line| line.split(/\t/) }
     end
   end
 end

data/lib/vienna_rna/modules/graphing.rb

@@ -14,19 +14,24 @@ module ViennaRna
           graph do |r|
             r.assign("line_graph.x", data.map(&:first))
             r.assign("line_graph.y", data.map(&:last))
-
-            if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
-              r.eval <<-STR
-                pdf("#{filename}", 6, 6)
-                plot(line_graph.x, line_graph.y, xlab = "#{x_label}", ylab = "#{y_label}", main = "#{title || 'Line Graph'}", type = "#{type}")
-                dev.off()
-              STR
-            else
-              r.eval <<-STR
-                quartz("Histogram", 6, 6)
-                plot(line_graph.x, line_graph.y, xlab = "#{x_label}", ylab = "#{y_label}", main = "#{title || 'Line Graph'}", type = "#{type}")
-              STR
-            end
+            
+            r.eval("%s('%s', 6, 6)" % [
+              writing_file?(filename) ? "pdf" : "quartz", 
+              writing_file?(filename) ? filename : "Graph", 
+            ])
+            
+            r.eval <<-STR
+              plot(
+                line_graph.x, 
+                line_graph.y, 
+                xlab = "#{x_label}", 
+                ylab = "#{y_label}", 
+                main = "#{title || 'Line Graph'}", 
+                type = "#{type}"
+              )
+            STR
+            
+            r.eval("dev.off()") if writing_file?(filename)
           end
         end
         
@@ -38,18 +43,68 @@ module ViennaRna
           graph do |r|
             r.assign("histogram.data", data)
             r.assign("histogram.breaks", breaks)
-
-            if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
+            
+            r.eval("%s('%s', 6, 6)" % [
+              writing_file?(filename) ? "pdf" : "quartz", 
+              writing_file?(filename) ? filename : "Histogram", 
+            ])
+            
+            r.eval <<-STR
+              hist(
+                histogram.data, 
+                breaks = histogram.breaks, 
+                xlab   = "#{x_label} (width: #{bin_size})", 
+                main   = "#{title || 'Histogram'}", 
+                freq   = #{relative ? 'FALSE' : 'TRUE'}
+              )
+            STR
+            
+            r.eval("dev.off()") if writing_file?(filename)
+          end
+        end
+        
+        def matrix_heatmap(x, y, z, title: nil, x_label: "Column index", y_label: "Row index", filename: false, num_colors: 64)
+          graph do |r|
+            if r.pull("ifelse('Matrix' %in% rownames(installed.packages()), 1, -1)") > 0
+              if forced_square = (x.max != y.max)
+                x << [x, y].map(&:max).max
+                y << [x, y].map(&:max).max
+                z << 0
+              end
+              
+              r.assign("matrix.i", x)
+              r.assign("matrix.j", y)
+              r.assign("matrix.x", z)
               r.eval <<-STR
-                pdf("#{filename}", 6, 6)
-                hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}", freq = #{relative ? 'FALSE' : 'TRUE'})
-                dev.off()
+                require("Matrix")
+                matrix.data <- sparseMatrix(
+                i      = matrix.i,
+                j      = matrix.j,
+                x      = matrix.x,
+                index1 = F
+                )
               STR
+              
+              generate_graph("Heatmap") do
+                <<-STR
+                  filtered.values <- Filter(function(i) { is.finite(i) & i != 0 }, matrix.x)
+                  print(apply(as.matrix(matrix.data), 2, rev))
+                  print(c(sort(filtered.values)[2], max(filtered.values)))
+                
+                  image(
+                    x    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])), 
+                    y    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])), 
+                    z    = as.matrix(matrix.data),
+                    col  = rev(heat.colors(#{num_colors})),
+                    zlim = #{forced_square ? "c(sort(filtered.values)[2], max(filtered.values))" : "c(min(filtered.values), max(filtered.values))"},
+                    xlab = "#{x_label} (1-indexed)",
+                    ylab = "#{y_label} (1-indexed)"
+                  )
+                  title("#{title || 'Matrix Heatmap'}")
+                STR
+              end
             else
-              r.eval <<-STR
-                quartz("Histogram", 6, 6)
-                hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}", freq = #{relative ? 'FALSE' : 'TRUE'})
-              STR
+              puts "Please install the Matrix package for R before using this function."
             end
           end
         end
@@ -75,17 +130,24 @@ module ViennaRna
           # plot([{ x: roc_curve.map(&:first), y: roc_curve.map(&:last), style: "lines" }], options)
         end
         
-        # def quick_plot(data, title = "", options = {})
-        #   quick_overlay([{ data: data }], title, options)
-        # end
+        private
         
-        # def quick_overlay(data, title = "", options = {})
-        #   # [{ data: [[x_0, y_0], [x_1, y_1], ...], label: "Label" }, { data: [[x_0, y_0], [x_1, y_1], ...] }]
-        #   options[:plot] = ((options[:plot] || {}).merge(title: title))
-        #   options.merge!(output: "file") if options[:filename]
+        def generate_graph(window_title = "ViennaRNA Graph in R", &block)
+          r, filename = block.binding.eval("[r, filename]")
           
-        #   plot(data.map { |hash| { title: hash[:label], x: hash[:data].map(&:first), y: hash[:data].map(&:last), style: "linespoints" }.merge(hash[:options] || {}) }, options)
-        # end
+          r.eval("%s('%s', 6, 6)" % [
+            writing_file?(filename) ? "pdf" : "quartz", 
+            writing_file?(filename) ? filename : window_title, 
+          ])
+          
+          r.eval(yield)
+          
+          r.eval("dev.off()") if writing_file?(filename)
+        end
+        
+        def writing_file?(filename)
+          filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
+        end
       end
     end
 

data/lib/vienna_rna/modules/rna.rb

@@ -40,6 +40,8 @@ module ViennaRna
           raw_data:         rna.raw_data
         )
       end
+      
+      alias_method :placeholder, :new
     end
     
     def initialize(sequence: "", structure: "", second_structure: "", raw_data: {})
@@ -70,16 +72,13 @@ module ViennaRna
     alias :str_1 :structure
     alias :str_2 :second_structure
     
-    def inspect
-      "#<%s>" % [
-        "#{self.class.name}",
-        ("#{seq[0, 20]   + (seq.length > 20   ? '...' : '')}"          if seq),
-        ("#{str_1[0, 20] + (str_1.length > 20 ? ' [truncated]' : '')}" if str_1),
-        ("#{str_2[0, 20] + (str_2.length > 20 ? ' [truncated]' : '')}" if str_2),
-      ].compact.join(" ")
+    def empty_structure
+      "." * seq.length
     end
+
+    alias :empty_str :empty_structure
     
-    def write_fa!(filename, comment = "")
+    def write_fa!(filename, comment = nil)
       filename.tap do |filename|
         File.open(filename, ?w) do |file|
           file.write("> %s\n" % comment) if comment
@@ -102,10 +101,13 @@ module ViennaRna
       end
     end
 
-    def empty_structure
-      "." * seq.length
+    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(" ")
     end
-
-    alias :empty_str :empty_structure
   end
 end

data/lib/vienna_rna/modules/rna2dfold.rb

@@ -0,0 +1,25 @@
+module ViennaRna
+  class Rna2dfold < EnergyGrid2d
+    BASE_FLAGS = {
+      d:         0,
+      p:         :empty,
+      "-noBT" => :empty
+    }
+
+    self.executable_name = "RNA2Dfold"
+
+    def run_command(flags = {})
+      ViennaRna.debugger { "Running RNA2Dfold on #{data.inspect}" }
+      
+      "cat %s  | %s %s" % [
+        data.temp_fa_file!,
+        exec_name, 
+        stringify_flags(BASE_FLAGS.merge(self.class.const_defined?(:FLAGS) ? self.class.const_get(:FLAGS) : {}).merge(flags))
+      ]
+    end
+    
+    def distribution
+      response.split(/\n/)[6..-1].map { |line| line.split(/\t/).at_indexes([0, 1, 2, 6]) }
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.8.6
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-23 00:00:00.000000000 Z
+date: 2013-09-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -102,6 +102,7 @@ extra_rdoc_files: []
 files:
 - lib/vienna_rna/modules/base.rb
 - lib/vienna_rna/modules/batch.rb
+- lib/vienna_rna/modules/energy_grid_2d.rb
 - lib/vienna_rna/modules/eval.rb
 - lib/vienna_rna/modules/fftbor.rb
 - lib/vienna_rna/modules/fftbor2d.rb
@@ -112,6 +113,7 @@ files:
 - lib/vienna_rna/modules/heat.rb
 - lib/vienna_rna/modules/parser.rb
 - lib/vienna_rna/modules/rna.rb
+- lib/vienna_rna/modules/rna2dfold.rb
 - lib/vienna_rna/modules/rna_extensions.rb
 - lib/vienna_rna/modules/rnabor.rb
 - lib/vienna_rna/modules/subopt.rb