vienna_rna 0.1.5 → 0.1.6

data/README.md

@@ -0,0 +1,11 @@
+A simple gem for facilitating bindings to the ViennaRNA package (http://www.tbi.univie.ac.at/~ivo/RNA/). Note that this gem makes no effort to build and install the ViennaRNA suite locally at this time, and instead relies on its presence on the host machine. Leverages the BioRuby gem (http://bioruby.open-bio.org/) libraries for file parsing.
+
+Simple use case:
+ruby-1.9.3-p125 :001 > require "vienna_rna"
+ => true 
+ruby-1.9.3-p125 :002 > rna = ViennaRna::Fold.run(seq: "CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG")
+ => #<ViennaRna::Fold:0x007f9c48839dc0>
+ruby-1.9.3-p125 :003 > rna.structure
+ => "((((..(((...(((....))).)))..))))" 
+ruby-1.9.3-p125 :004 > rna.mfe
+ => -19.7

data/lib/vienna_rna/modules/base.rb

@@ -2,25 +2,6 @@ require "benchmark"
 
 module ViennaRna
   class Base
-    class Rna
-      attr_reader :sequence, :structure
-      
-      def initialize(sequence, structure = nil)
-        @sequence  = sequence
-        @structure = (structure == :mfe ? ViennaRna::Fold.run(seq).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
@@ -69,7 +50,12 @@ module ViennaRna
     end
     
     def exec_sequence_format
-      data.seq
+      if data.str
+        '"%s
+        %s"' % [data.seq, data.str]
+      else
+        data.seq
+      end
     end
     
     def initialize(data)
@@ -104,14 +90,18 @@ module ViennaRna
     end
     
     def stringify_flags(flags)
-      flags.inject("") { |string, (flag, value)| (string + (value == :empty ? " -%s" % flag : " -%s %s" % [flag, value])).strip }
+      base_flags = self.class.const_defined?(:BASE_FLAGS) ? self.class.const_get(:BASE_FLAGS) : {}
+      
+      flags.merge(base_flags).inject("") do |string, (flag, value)| 
+        (string + (value == :empty ? " -%s" % flag : " -%s %s" % [flag, value])).strip
+      end
     end
     
     def run(flags = {})
       command = if respond_to?(:run_command)
         method(:run_command).arity.zero? ? run_command : run_command(flags)
       else
-        "echo #{exec_sequence_format} | #{exec_name} -noPS #{stringify_flags(flags)}"
+        "echo #{exec_sequence_format} | #{exec_name} #{stringify_flags(flags)}"
       end
       
       debugger { command }

data/lib/vienna_rna/modules/eval.rb

@@ -0,0 +1,9 @@
+module ViennaRna
+  class Eval < Base
+    attr_reader :mfe
+    
+    def post_process
+      @mfe = Parser.mfe(@response)
+    end
+  end
+end

data/lib/vienna_rna/modules/fold.rb

@@ -1,14 +1,18 @@
 module ViennaRna
   class Fold < Base
+    BASE_FLAGS = {
+      "-noPS" => :empty
+    }
+    
     attr_reader :structure, :mfe
     
     def post_process
-      structure = @response.split(/\n/).last.gsub(/ \(\s*(-?\d*\.\d*)\)$/, "")
+      structure = @response.split(/\n/).last.gsub(Parser::REGEXP[:mfe], "")
       
       unless data.seq.length == structure.length
         raise "Sequence: '#{data.seq}'\nStructure: '#{structure}'"
       else
-        @structure, @mfe = structure, $1.to_f
+        @structure, @mfe = structure, Parser.mfe(@response)
       end
     end
     

data/lib/vienna_rna/modules/parser.rb

@@ -0,0 +1,13 @@
+module ViennaRna
+  module Parser
+    REGEXP = {
+      mfe: / \(\s*(-?\d*\.\d*)\)$/
+    }
+    
+    class << self
+      def mfe(response)
+        response.split(/\n/).last.match(REGEXP[:mfe])[1].to_f
+      end
+    end
+  end
+end

data/lib/vienna_rna/modules/rna.rb

@@ -0,0 +1,21 @@
+module ViennaRna
+  class Rna
+    attr_reader :sequence, :structure
+      
+    def initialize(sequence, structure = nil)
+      @sequence  = sequence
+      @structure = (structure == :mfe ? ViennaRna::Fold.run(seq).structure : structure)
+    end
+
+    alias :seq :sequence
+    alias :str :structure
+      
+    def safe_structure
+      structure || empty_structure
+    end
+      
+    def empty_structure
+      "." * seq.length
+    end
+  end
+end

data/lib/vienna_rna/modules/xbor.rb

@@ -35,9 +35,9 @@ module ViennaRna
       full_distribution.each_with_index.to_a.map(&:reverse)[0..data.seq.length]
     end
     
-    def quick_plot
+    def quick_plot(title = nil)
       ViennaRna::Utils.quick_plot(
-        "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure], 
+        title || "%s\\n%s\\n%s" % [self.class.name, data.seq, data.safe_structure], 
         k_p_points
       )
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-25 00:00:00.000000000 Z
+date: 2012-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -49,16 +49,20 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- ./lib/vienna_rna/modules/base.rb
-- ./lib/vienna_rna/modules/batch.rb
-- ./lib/vienna_rna/modules/fftbor.rb
-- ./lib/vienna_rna/modules/fold.rb
-- ./lib/vienna_rna/modules/heat.rb
-- ./lib/vienna_rna/modules/rnabor.rb
-- ./lib/vienna_rna/modules/subopt.rb
-- ./lib/vienna_rna/modules/utils.rb
-- ./lib/vienna_rna/modules/xbor.rb
-- ./lib/vienna_rna.rb
+- lib/vienna_rna/modules/base.rb
+- lib/vienna_rna/modules/batch.rb
+- lib/vienna_rna/modules/eval.rb
+- lib/vienna_rna/modules/fftbor.rb
+- lib/vienna_rna/modules/fold.rb
+- lib/vienna_rna/modules/heat.rb
+- lib/vienna_rna/modules/parser.rb
+- lib/vienna_rna/modules/rna.rb
+- lib/vienna_rna/modules/rnabor.rb
+- lib/vienna_rna/modules/subopt.rb
+- lib/vienna_rna/modules/utils.rb
+- lib/vienna_rna/modules/xbor.rb
+- lib/vienna_rna.rb
+- README.md
 homepage: http://rubygems.org/gems/vienna_rna
 licenses: []
 post_install_message: