vienna_rna 0.1.2 → 0.1.3

data/lib/modules/base.rb

@@ -7,7 +7,7 @@ module ViennaRna
       
       def initialize(sequence, structure = nil)
         @sequence  = sequence
-        @structure = structure
+        @structure = (structure == :mfe ? ViennaRna::Fold.run(seq).structure : structure)
       end
 
       alias :seq :sequence
@@ -75,6 +75,7 @@ module ViennaRna
     def initialize(data)
       @data = case data
       when Bio::FastaFormat then data
+      when Rna              then data
       when String           then Rna.new(data)
       when Hash             then Rna.new(data[:sequence] || data[:seq], data[:structure] || data[:str])
       end
@@ -106,7 +107,7 @@ module ViennaRna
       command = if respond_to?(:run_command)
         method(:run_command).arity.zero? ? run_command : run_command(flags)
       else
-        "echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}"
+        "echo #{exec_sequence_format} | #{exec_name} -noPS #{stringify_flags(flags)}"
       end
       
       debugger { command }

data/lib/modules/fftbor.rb

@@ -1,17 +1,16 @@
 require "tempfile"
 require "bigdecimal"
+require "diverge"
 
 module ViennaRna
   class Fftbor < Xbor
     MODES = {
-      dispatch:   "TripletPF",
-      standalone: "Fftbor"
+      dispatch:   "RNAcentral",
+      standalone: "FFTbor"
     }
     
     def run_command(flags = {})
-      flags = { mode: :dispatch }.merge(flags)
-      
-      ap flags
+      flags = { mode: :standalone }.merge(flags)
       
       unless MODES[flags[:mode]]
         STDERR.puts "ERROR: The mode requested (%s) is not available" % flags[:mode]
@@ -21,7 +20,7 @@ module ViennaRna
       when :standalone then
         super(flags)
       when :dispatch then
-        "./%s -m 6 -tr 0 -s %s -ss '%s'" % [MODES[flags[:mode]], data.seq, data.safe_structure]
+        "%s -m 6 -tr 0 -s %s -ss '%s'" % [MODES[flags[:mode]], data.seq, data.safe_structure]
       end
     end
     
@@ -38,5 +37,14 @@ module ViennaRna
     def distribution
       self.class.parse(response).map { |row| BigDecimal.new(row[1]) }
     end
+    
+    def compare
+      {
+        dispatch:   self.class.new(data).run(mode: :dispatch).distribution,
+        standalone: self.class.new(data).run(mode: :standalone).distribution
+      }.tap do |hash|
+        hash[:tvd] = Diverge.new(hash[:dispatch], hash[:standalone]).tvd
+      end
+    end
   end
 end

data/lib/modules/utils.rb

@@ -1,3 +1,6 @@
+require "matrix"
+require "gnuplot"
+
 module ViennaRna
   module Utils
     class << self
@@ -21,6 +24,34 @@ module ViennaRna
           end
         end
       end
+
+      def regress(x, y, degree)
+        x_data   = x.map { |i| (0..degree).map { |power| i ** power.to_f } }
+        x_matrix = Matrix[*x_data]
+        y_matrix = Matrix.column_vector(y)
+
+        ((x_matrix.transpose * x_matrix).inverse * x_matrix.transpose * y_matrix).transpose.to_a[0]
+      end
+      
+      def plot(data, options = {})
+        options = { title: "Title", x_label: "X Axis", y_label: "Y Axis" }.merge(options)
+        
+        Gnuplot.open do |gnuplot|
+          Gnuplot::Plot.new(gnuplot) do |plot|
+
+            plot.title(options[:title])
+            plot.xlabel(options[:x_label])
+            plot.ylabel(options[:y_label])
+
+            plot.data = data.map do |data_hash|
+              Gnuplot::DataSet.new([data_hash[:x], data_hash[:y]]) do |dataset|
+                dataset.with = "points"
+                data_hash[:title] ? dataset.title = data_hash[:title] : dataset.notitle
+              end
+            end
+          end
+        end
+      end
     end
   end
 end

data/lib/modules/xbor.rb

@@ -11,7 +11,7 @@ module ViennaRna
       file.write("%s\n" % data.safe_structure)
       file.close
       
-      "./%s -nodangle %s" % [exec_name, file.path]
+      "%s -nodangle -E /usr/local/bin/energy.par %s" % [exec_name, file.path]
     end
     
     def self.parse(response)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-29 00:00:00.000000000 Z
+date: 2012-07-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio