vienna_rna 0.13.0 → 0.14.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,6 +1,8 @@
 ViennaRna
 ------------------------
 
+[![Gem Version](https://badge.fury.io/rb/vienna_rna.png)](http://badge.fury.io/rb/vienna_rna)
+
 A simple gem for facilitating bindings to the ViennaRNA package (http://www.tbi.univie.ac.at/~ivo/RNA/), amongst other RNA packages. 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. Also includes a lot of utilities surrounding RNA sequence / structure parsing, graphing using R (via RinRuby) and other analysis tools. Used privately as the foundation for much of the research I do at http://bioinformatics.bc.edu/clotelab/
 
 Simple use case:

data/lib/vienna_rna.rb

@@ -63,8 +63,8 @@ unless defined? RNA
 end
 
 module RNA
-  def self.load_all(pattern: "*.fa")
-    Dir[pattern].map { |file| RNA.from_fasta(file) }
+  def self.load_all(pattern = "*.fa")
+    Dir[File.directory?(pattern) ? pattern + "/*.fa" : pattern].map { |file| RNA.from_fasta(file) }
   end
   
   def self.random(size, *args)

data/lib/vienna_rna/global/rna.rb

@@ -140,7 +140,7 @@ module ViennaRna
           ("#{seq[0, 20]   + (seq.length > 20   ? '... [%d]' % seq.length : '')}" if seq   && !seq.empty?),
           ("#{str_1[0, 20] + (str_1.length > 20 ? ' [%d]'    % seq.length : '')}" if str_1 && !str_1.empty?),
           ("#{str_2[0, 20] + (str_2.length > 20 ? ' [%d]'    % seq.length : '')}" if str_2 && !str_1.empty?),
-          (!name.empty? ? name : "#{self.class.name}")
+          (name ? name : "#{self.class.name}")
         ].compact.join(", ")
       end
     end

data/lib/vienna_rna/package/fftbor2d.rb

@@ -2,43 +2,18 @@ module ViennaRna
   module Package
     class Fftbor2d < EnergyGrid2d
       self.executable_name = "FFTbor2D"
-      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
+      self.default_flags   = ->(_, flags) { (flags.keys & %i|M S|).empty? ? { S: :empty } : {} }
 
       def run_command(flags)
         ViennaRna.debugger { "Running #{exec_name} on #{data.inspect}" }
-      
+
         "%s %s %s" % [
-          exec_name, 
+          exec_name,
           stringify_flags(flags),
           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/) }
       end

data/lib/vienna_rna/package/plot.rb

@@ -0,0 +1,19 @@
+module ViennaRna
+  module Package
+    class Plot < Base
+      self.call_with     = [ :comment, :seq, :str]
+      self.default_flags = {
+        t: 0,
+        o: "svg"
+      }
+
+      def run_command(flags)
+        "cat %s | %s %s" % [
+          data.temp_fa_file!,
+          exec_name,
+          stringify_flags(flags)
+        ]
+      end
+    end
+  end
+end

data/lib/vienna_rna/package/population.rb

@@ -0,0 +1,38 @@
+module ViennaRna
+  module Package
+    class Population < Base
+      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}" }
+
+        "%s %s %s" % [
+          exec_name,
+          stringify_flags(flags),
+          data.temp_fa_file!
+        ]
+      end
+
+      def post_process
+        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
+  end
+end

data/lib/vienna_rna/package/subopt.rb

@@ -2,11 +2,18 @@ module ViennaRna
   module Package
     class Subopt < Base
       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 do |output|
+          structure, mfe = output.split(/\s+/)
+
+          RNA.from_string(data.seq, structure).tap do |rna|
+            rna.instance_variable_set(:@mfe, mfe.to_f)
+            rna.class_eval { attr_reader :mfe }
+          end
+        end
       end
-    
+
       def bin(count = 1)
         run(p: count).structures.inject(Hash.new { |hash, key| hash[key] = 0 }) do |hash, structure|
           hash.tap do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.13.0
+  version: 0.14.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-06 00:00:00.000000000 Z
+date: 2014-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.2'
+        version: '4.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.2'
+        version: '4.0'
 - !ruby/object:Gem::Dependency
   name: shuffle
   requirement: !ruby/object:Gem::Requirement
@@ -111,6 +111,8 @@ files:
 - lib/vienna_rna/package/heat.rb
 - lib/vienna_rna/package/kinwalker.rb
 - lib/vienna_rna/package/mfpt.rb
+- lib/vienna_rna/package/plot.rb
+- lib/vienna_rna/package/population.rb
 - lib/vienna_rna/package/rna2dfold.rb
 - lib/vienna_rna/package/rnabor.rb
 - lib/vienna_rna/package/spectral.rb
@@ -118,7 +120,8 @@ files:
 - lib/vienna_rna/package/tabu_path.rb
 - lib/vienna_rna/package/xbor.rb
 homepage: http://rubygems.org/gems/vienna_rna
-licenses: []
+licenses:
+- MIT
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -136,7 +139,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Bindings to the Vienna RNA package, and other major command line utilities