vienna_rna 0.0.5 → 0.0.6

data/lib/modules/base.rb

@@ -1,5 +1,26 @@
+require "benchmark"
+
 module ViennaRna
   class Base
+    class Rna
+      attr_reader :sequence, :structure
+      
+      def initialize(sequence, structure = nil)
+        @sequence  = sequence
+        @structure = structure
+      end
+
+      alias :seq :sequence
+      
+      def safe_structure
+        structure || empty_structure
+      end
+      
+      def empty_structure
+        "." * seq.length
+      end
+    end
+    
     class_attribute :executable_name
     
     class << self
@@ -33,29 +54,33 @@ module ViennaRna
       end
     end
     
-    attr_reader :fasta, :response
+    attr_reader :data, :response, :runtime
     
     def exec_name
       executable_name || "rna#{self.class.name.split('::').last.underscore}"
     end
     
     def exec_sequence_format
-      fasta.seq
+      data.seq
     end
     
     def initialize(data)
-      # Doesn't support structures on the third line yet.
-      @fasta = case data
+      @data = case data
       when Bio::FastaFormat then data
-      when String           then Bio::FastaFormat.new(data.split(/\n/).length > 1 ? data : ">\n%s" % data)
+      when String           then Rna.new(data)
+      when Hash             then Rna.new(data[:sequence] || data[:seq], data[:structure] || data[:str])
       end
     end
     
     def run_with_hooks(flags = {})
       tap do
-        pre_run_check unless respond_to?(:run_command)
-        @response = run_without_hooks(flags)
-        post_process if respond_to?(:post_process)
+        @runtime = Benchmark.measure do
+          pre_run_check unless respond_to?(:run_command)
+          @response = run_without_hooks(flags)
+          post_process if respond_to?(:post_process)
+        end
+        
+        puts "Total runtime: %.3f sec." % runtime.real if ViennaRna.debug
       end
     end
     

data/lib/modules/fftbor.rb

@@ -0,0 +1,48 @@
+module ViennaRna
+  class Fftbor < Base
+    attr_reader :flags
+    
+    def run_command(flags)
+      @flags = flags
+      
+      "./FFTbor -s %s -r %s -c %s -p %s" % [
+        data.seq, 
+        data.safe_structure,
+        flags[:scaling_factor] ||= 1,
+        flags[:precision] ||= 6
+      ]
+    end
+    
+    def parse_partition
+      response.split(/\n/).find { |line| line =~ /^Z\[1\]\[\d+\]:/ }.match(/^Z\[1\]\[\d+\]:\s*(.*)/)[1].to_f
+    end
+    
+    def parse_total_count
+      response.split(/\n/).find { |line| line =~ /^Z\[\d+\]\[1\]:/ }.match(/^Z\[\d+\]\[1\]:\s*(.*)/)[1].to_i
+    end
+    
+    def parse_points
+      self.class.parse(response, "ROOTS AND SOLUTIONS") { |line| line.strip.split(/\s\s+/).map { |value| eval("Complex(#{value})") } }
+    end
+    
+    def parse_distribution
+      if flags[:scaling_factor] != 1
+        puts "Warning: The scaling factor was set to #{flags[:scaling_factor]}. The Boltzmann distribution is not setup to handle scaling in this fashion."
+      end
+      
+      self.class.parse(response, "DISTRIBUTION") { |line| line.strip.split(/:\s*/).last.to_f }
+    end
+    
+    def self.parse(response, delimiter)
+      response.split(/\n/).reject do |line| 
+        line.empty?
+      end.drop_while do |line|
+        line !~ /^START #{delimiter}/i
+      end.reverse.drop_while do |line|
+        line !~ /^END #{delimiter}/i
+      end.reverse[1..-2].map do |line|
+        yield line
+      end
+    end
+  end
+end

data/lib/modules/fold.rb

@@ -5,8 +5,8 @@ module ViennaRna
     def post_process
       structure = @response.split(/\n/).last.gsub(/ \(\s*(-?\d*\.\d*)\)$/, "")
       
-      unless fasta.seq.length == structure.length
-        raise "Sequence: '#{fasta.seq}'\nStructure: '#{structure}'"
+      unless data.seq.length == structure.length
+        raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
       else
         @structure, @mfe = structure, $1.to_f
       end

data/lib/modules/rnabor.rb

@@ -1,45 +1,38 @@
+require "tempfile"
+
 module ViennaRna
   class Rnabor < Base
     def run_command(flags)
-      "./RNAbor -s %s -c %s" % [fasta.seq, flags[:scaling_factor] || 1]
+      file = Tempfile.new("rna")
+      file.write("%s\n" % data.seq)
+      file.write("%s\n" % data.safe_structure)
+      file.close
+      
+      "./RNAbor %s" % file.path
     end
     
-    def parse_total_count
-      response.split(/\n/).find { |line| line =~ /^Z\[\d+\]\[1\]:/ }.match(/^Z\[\d+\]\[1\]:\s*(.*)/)[1].to_i
+    def parse_partition
+      parse_non_zero_shells.sum
     end
     
-    def parse_points
-      self.class.parse(response, "ROOTS AND SOLUTIONS") { |line| line.strip.split(/\s\s+/).map { |value| eval("Complex(#{value})") } }
+    def parse_total_count
+      parse_counts.sum
     end
     
     def parse_counts
-      self.class.parse(response, "UNSCALED SUM") { |line| line.strip.split(/:\s*/).map(&:to_f) }
+      (non_zero_counts = self.class.parse(response).map { |row| row[2].to_i }) + [0] * (data.seq.length - non_zero_counts.length + 1)
     end
     
-    def in_r(options = {})
-      results = solve_in_r(options).processed_response
-      
-      options[:unscale] ? results.map { |i| i * parse_total_count } : results
+    def parse_distribution
+      (non_zero_distribution = parse_non_zero_shells.map { |i| i / parse_partition }) + [0.0] * (data.seq.length - non_zero_distribution.length + 1)
     end
     
-    def solve_in_r(options = {})
-      options = { precision: 0, unscale: false }.merge(options)
-      
-      run unless response
-      
-      ViennaRna::FftInR.new(parse_points.map(&:last), parse_total_count, options[:precision]).run
+    def parse_non_zero_shells
+      self.class.parse(response).map { |row| row[1].to_f }
     end
     
-    def self.parse(response, delimiter)
-      response.split(/\n/).reject do |line| 
-        line.empty?
-      end.drop_while do |line|
-        line !~ /^START #{delimiter}/i
-      end.reverse.drop_while do |line|
-        line !~ /^END #{delimiter}/i
-      end.reverse[1..-2].map do |line|
-        yield line
-      end
+    def self.parse(response)
+      response.split(/\n/)[2..-1].map { |line| line.split(/\t/) }
     end
   end
 end

data/lib/modules/utils.rb

@@ -1,5 +1,3 @@
-# "/Users/evansenter/Source/mirna_5.1/hairpin.fa"
-
 module ViennaRna
   module Utils
     class << self

data/lib/vienna_rna.rb

@@ -10,12 +10,12 @@ end
 
 module Enumerable
   def sum
-    inject { |sum, i| sum + i }
+    inject(&:+)
   end
 end
 
 module ViennaRna
-  @debug = false
+  @debug = true
   
   def self.const_missing(name)
     if Base.exec_exists?(name)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors:
@@ -49,24 +49,16 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- !binary |-
-  Li9saWIvbW9kdWxlcy9iYXNlLnJi
-- !binary |-
-  Li9saWIvbW9kdWxlcy9iYXRjaC5yYg==
-- !binary |-
-  Li9saWIvbW9kdWxlcy9mZnRfaW5fci5yYg==
-- !binary |-
-  Li9saWIvbW9kdWxlcy9mb2xkLnJi
-- !binary |-
-  Li9saWIvbW9kdWxlcy9oZWF0LnJi
-- !binary |-
-  Li9saWIvbW9kdWxlcy9ybmFib3IucmI=
-- !binary |-
-  Li9saWIvbW9kdWxlcy9zdWJvcHQucmI=
-- !binary |-
-  Li9saWIvbW9kdWxlcy91dGlscy5yYg==
-- !binary |-
-  Li9saWIvdmllbm5hX3JuYS5yYg==
+- ./lib/modules/base.rb
+- ./lib/modules/batch.rb
+- ./lib/modules/fft_in_r.rb
+- ./lib/modules/fftbor.rb
+- ./lib/modules/fold.rb
+- ./lib/modules/heat.rb
+- ./lib/modules/rnabor.rb
+- ./lib/modules/subopt.rb
+- ./lib/modules/utils.rb
+- ./lib/vienna_rna.rb
 homepage: http://rubygems.org/gems/vienna_rna
 licenses: []
 post_install_message: 
@@ -92,3 +84,4 @@ signing_key:
 specification_version: 3
 summary: Bindings to the Vienna RNA package.
 test_files: []
+has_rdoc: