wrnap 1.2.0 → 1.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b2cc53a30fd53e8dc635b9a6f0e6b9dfc985eefb
-  data.tar.gz: ce9692b9164e77fac7b6d4e56ed6398500c19e71
+  metadata.gz: f2efcb65abde80f14ce6f0e5eba3d5438b23ba33
+  data.tar.gz: 6c7873c5b0936b137a7f0f957f4853bcdc48d345
 SHA512:
-  metadata.gz: 6e5c9b208ddb20f3d9377a40bfa6e5467a35c9012ddd0a0e38bcb47f082de147bd82df8ef7040a9dad2910f87f6bcc18df79b0f187a142f5ba99afa6bcc76d17
-  data.tar.gz: cf74fe53fde6cbdf70a7430d6dee2e56cbbcd12ad64b9a9e6c11a68e279b7a46657ffd2fe1b5d5ed9d813e223016f27479a638b72e8f05537ed1f0762cb22f92
+  metadata.gz: aa223b71c6b69f3207ebf76b4b34b90a73d4686293adc10579936d3ac609247648ff62dd1f4cf529ac6be9b8fa28010151c673c39c6d0ef4040ecacc07a3875f
+  data.tar.gz: 3808f6f38a0c3a9a5877e3d829afab5fe11766d31dd55a1091207a774dfa31b87d3b4376a1baaf1adc15c396d6cc85f403e4af30eb031a5f5f83964ee5bf4b88

data/lib/wrnap/package/fft_eq.rb

@@ -8,12 +8,13 @@ module Wrnap
           "-fftbor2d-i"   => context.data.seq,
           "-fftbor2d-j"   => context.data.str_1,
           "-fftbor2d-k"   => context.data.str_2,
-          "-population-e" => 1e-4
+          "-population-q" => true
         }
       end
 
       def post_process
-        @equilibrium = (response.empty? || response =~ /Infinity/ ? -1 : 10 ** response.strip.to_f)
+        raw_eq_time  = (response.match(/index\tlogtime\n\d+\t(.*)\n/) || [])[1] || ""
+        @equilibrium = (raw_eq_time =~ /^(|-?Infinity)$/ ? -1 : 10 ** raw_eq_time.to_f)
       end
     end
   end

data/lib/wrnap/package/fft_mfpt.rb

@@ -11,7 +11,7 @@ module Wrnap
           "-fftbor2d-i" => context.data.seq,
           "-fftbor2d-j" => context.data.str_1,
           "-fftbor2d-k" => context.data.str_2,
-          "-mfpt-x"     => true
+          "X"           => true
         }
       end
       self.quote_flag_params = %w|-fftbor2d-i -fftbor2d-j -fftbor2d-k|

data/lib/wrnap/package/fftbor2d.rb

@@ -2,12 +2,12 @@ module Wrnap
   module Package
     class Fftbor2d < EnergyGrid2d
       self.executable_name = "FFTbor2D"
-      self.default_flags   = ->(_, flags) { (flags.keys & %i|M S|).empty? ? { S: :empty } : {} }
+      self.default_flags   = ->(_, flags) { (flags.keys & %i|m s|).empty? ? { s: :empty } : {} }
 
       def run_command(flags)
         Wrnap.debugger { "Running #{exec_name} on #{data.inspect}" }
 
-        "%s %s %s" % [
+        "%s %s -f %s" % [
           exec_name,
           stringify_flags(flags),
           data.temp_fa_file!
@@ -15,7 +15,7 @@ module Wrnap
       end
 
       def distribution
-        response.split(/\n/).map { |line| line.split(/\t/) }
+        response.split(/\n/).map { |line| line.scanf("%d\t%d\t%f\t%f") }
       end
     end
   end

data/lib/wrnap/rna/box.rb

@@ -1,6 +1,7 @@
 module Wrnap
   class Rna
     class Box
+      prepend MetaMissing
       extend Forwardable
       include Enumerable
       include Wrnap::Global::Yaml
@@ -9,7 +10,10 @@ module Wrnap
 
       class << self
         def load_all(pattern = "*.fa", &block)
-          new(Dir[File.directory?(pattern) ? pattern + "/*.fa" : pattern].inject([]) { |array, file| array + RNA.from_fasta(file, &block).rnas })
+          new(Dir[File.directory?(pattern) ? File.join(pattern, "*.fa") : pattern].inject([]) do |array, file| 
+            loaded_rnas = RNA.from_fasta(file, &block)
+            array + (loaded_rnas.is_a?(Box) ? loaded_rnas.rnas : [loaded_rnas])
+          end)
         end
       end
 
@@ -47,10 +51,8 @@ module Wrnap
         klass == Array ? true : super
       end
       
-      def method_missing(name, *args, &block)
-        if (name_str = "#{name}") =~ /^run_\w+$/
-          run_in_parallel(name_str, *args)
-        else super end
+      handle_methods_like(/^run_\w+$/) do |match, name, *args, &block|
+        run_in_parallel(name, *args)
       end
 
       def inspect

data/lib/wrnap/rna/constraints.rb

@@ -1,3 +1,5 @@
+require File.join(File.dirname(__FILE__), "tree.rb")
+
 module Wrnap
   class Rna
     module Constraints
@@ -22,6 +24,8 @@ module Wrnap
       end
 
       class ConstraintBox
+        prepend MetaMissing
+        
         attr_reader :rna, :constraints
 
         def initialize(rna)
@@ -100,21 +104,19 @@ module Wrnap
           end
         end
         
-        alias :mask :to_s
+        alias_method :mask, :to_s
 
-        def method_missing(name, *args, &block)
-          method_name = name.to_s
+        handle_methods_like(TreeStem::STEM_NOTATION_REGEX) do |match, name, *args, &block|
+          rna.trunk.send(name.to_s)
+        end
+        
+        handle_methods_like(/^(prohibit|force)(_(left|right)_stem)?$/) do |match, name, *args, &block|
+          side_symbol = match[3] ? match[3].to_sym : :both
           
-          if method_name =~ TreeStem::STEM_NOTATION_REGEX
-            rna.trunk.send(method_name)
-          elsif mask_type = method_name.match(/^(prohibit|force)(_(left|right)_stem)?$/)
-            side_symbol = mask_type[3] ? mask_type[3].to_sym : :both
-
-            case mask_type[1]
-            when "prohibit" then mask!(args[0], side: side_symbol, symbol: args[1] || ?x)
-            when "force"    then mask!(args[0], side: side_symbol, symbol: args[1] || "()")
-            end
-          else super end
+          case match[1]
+          when "prohibit" then mask!(args[0], side: side_symbol, symbol: args[1] || ?x)
+          when "force"    then mask!(args[0], side: side_symbol, symbol: args[1] || "()")
+          end
         end
       end
 

data/lib/wrnap/rna/context.rb

@@ -40,10 +40,9 @@ module Wrnap
         end
 
         super(
-          sequence:         self.sequence,
-          structure:        options[:rna][:structure]        || options[:rna][:str_1] || options[:rna][:str],
-          second_structure: options[:rna][:second_structure] || options[:rna][:str_2],
-          comment:          options[:rna][:comment]          || options[:rna][:name] || identifier,
+          sequence:   self.sequence,
+          structures: options[:rna][:structures] || options[:rna][:structure] || options[:rna][:strs] || options[:rna][:str],
+          comment:    options[:rna][:comment] || options[:rna][:name] || identifier,
           &block
         )
 
@@ -94,7 +93,7 @@ module Wrnap
         !plus_strand?
       end
 
-      def sequence
+      alias_method :seq, def sequence
         if @raw_sequence
           @raw_sequence
         else
@@ -102,8 +101,6 @@ module Wrnap
           @raw_sequence   = (minus_strand? ? entrez_sequence.complement : entrez_sequence).upcase
         end
       end
-
-      alias :seq :sequence
       
       def_delegator :@raw_sequence, :length, :len
 

data/lib/wrnap/rna/extensions.rb

@@ -46,6 +46,11 @@ module Wrnap
         end
         
         def local_structural_shuffle(dishuffle: false)
+          # Permutes the base pairs of the structure provided for the template sequence independently of the unpaired regions, as in
+          # global_structural_shuffle. This adds the additional constraint that loops and helices are permuted as individual sets,
+          # rather than using two global loop / helix bags.
+          raise "the structural_shuffle functions require the initial RNA to have a structure" unless str
+          
           sequence       = " " * len
           loops, helices = loops_and_helices
         
@@ -69,6 +74,10 @@ module Wrnap
         end
         
         def global_structural_shuffle
+          # Permutes the nucleotides of the sequence such that the basepairs in the initial structure are shuffled independently of the
+          # unpaired bases. This ensures that the resulting sequence is compatible with the original structure.
+          raise "the structural_shuffle functions require the initial RNA to have a structure" unless str
+          
           sequence         = " " * len
           loops, helices   = loops_and_helices
           shuffled_loops   = Shuffle.new(loops.map { |loop| loop.in(seq) }.join.split(//)).shuffle

data/lib/wrnap/rna/metadata.rb

@@ -28,12 +28,10 @@ module Wrnap
           @__rna__, @__data__ = rna, {}
         end
 
-        def inspect
+        alias_method :to_s, def inspect
           "#<Metadata: %s>" % __data__.inspect
         end
 
-        alias :to_s :inspect
-
         def method_missing(name, *args, &block)
           case args.size
           when 0 then __data__[name]

data/lib/wrnap/rna/tree.rb

@@ -11,6 +11,7 @@ module Wrnap
     end
 
     class TreeStem < Tree::TreeNode
+      prepend MetaMissing
       extend Forwardable
       include Enumerable
 
@@ -19,6 +20,10 @@ module Wrnap
       def_delegators :@content, :i, :j, :k, :l
       def_delegator  :@content, :length, :stem_length
       
+      def in(sequence)
+        sequence[i..j]
+      end
+      
       def unpaired_regions
         Wrnap.debugger { "Collecting unpaired regions for %s" % [root.content.name] }
         
@@ -78,26 +83,27 @@ module Wrnap
         children.each { |child| child.postorder_traversal(&block) }
         yield self
       end
-
-      def method_missing(name, *args, &block)
-        if (method_name = name.to_s) =~ STEM_NOTATION_REGEX
-          call_type   = method_name[0]
-          indices     = method_name.gsub(/\D+/, ?_).split(?_).reject(&:empty?).map(&:to_i)
-          helix_index = method_name.match(/([ijkl])$/) ? $1 : ""
-
-          if indices.size > 1 && child = children[indices[0] - 1]
-            child.send(call_type + indices[1..-1].join(?_) + helix_index)
-          elsif child = children[indices[0] - 1]
-            case call_type
-            when ?p then helix_index.empty? ? child.content : child.send(helix_index)
-            when ?t then child
-            end
+      
+      handle_methods_like(STEM_NOTATION_REGEX) do |match, name, *args, &block|
+        method_name = name.to_s
+        call_type   = method_name[0]
+        indices     = method_name.gsub(/\D+/, ?_).split(?_).reject(&:empty?).map(&:to_i)
+        helix_index = method_name.match(/([ijkl])$/) ? $1 : ""
+
+        if indices.size > 1 && child = children[indices[0] - 1]
+          child.send(call_type + indices[1..-1].join(?_) + helix_index)
+        elsif child = children[indices[0] - 1]
+          case call_type
+          when ?p then helix_index.empty? ? child.content : child.send(helix_index)
+          when ?t then child
           end
-        else super end
+        end
       end
     end
 
     class TreePlanter
+      prepend MetaMissing
+      
       attr_reader :rna, :root
 
       def initialize(rna, tree = false)
@@ -144,7 +150,7 @@ module Wrnap
       end
 
       def coalesce
-        self.class.new(rna, root.dup).tap { |tree| tree.merge_interior_loops! }
+        self.class.new(rna, root.clone).tap { |tree| tree.merge_interior_loops! }
       end
 
       def coalesce!
@@ -152,7 +158,7 @@ module Wrnap
       end
       
       def fuse
-        self.class.new(rna, root.dup).tap { |tree| tree.extend_interior_loops! }
+        self.class.new(rna, root.clone).tap { |tree| tree.extend_interior_loops! }
       end
 
       def fuse!
@@ -194,16 +200,12 @@ module Wrnap
         root.print_tree and nil
       end
 
-      def inspect
+      alias_method :to_s, def inspect
         "#<TreePlanter: %s>" % depth_signature.inspect
       end
-
-      alias :to_s :inspect
-
-      def method_missing(name, *args, &block)
-        if name.to_s =~ TreeStem::STEM_NOTATION_REGEX
-          root.send(name, *args, &block)
-        else super end
+      
+      handle_methods_like(TreeStem::STEM_NOTATION_REGEX) do |match, name, *args, &block|
+        root.send(name, *args, &block)
       end
     end
   end

data/lib/wrnap/rna.rb

@@ -1,5 +1,6 @@
 module Wrnap
   class Rna
+    prepend MetaMissing
     extend Forwardable
     include Wrnap::Global::Yaml
     include Wrnap::Rna::Extensions
@@ -11,25 +12,28 @@ module Wrnap
     CANONICAL_BASES = Set.new << Set.new([?G, ?C]) << Set.new([?A, ?U]) << Set.new([?G, ?U])
 
     attr_accessor :comment
-    attr_reader :sequence, :structure, :second_structure, :metadata
+    attr_reader   :sequence, :structures, :metadata
 
     class << self
-      def init_from_string(sequence, structure = nil, second_structure = nil, comment = nil, &block)
-        new(
-          sequence:         sequence,
-          structure:        structure,
-          second_structure: second_structure,
-          comment:          comment,
-          &block
-        )
+      def init_from_string(sequence, *remaining_args, &block)
+        init_from_hash(parse_rna_attributes(sequence, remaining_args), &block)
+      end
+      
+      def parse_rna_attributes(sequence, attributes = [])
+        last_arg = (attributes = attributes.flatten).last
+        
+        if last_arg.is_a?(Symbol) || Regexp.compile("^[\\.\\(\\)]{%d}$" % sequence.length) =~ last_arg
+          { seq: sequence, strs: attributes }
+        else
+          { seq: sequence, strs: attributes[0..-2], comment: last_arg }
+        end
       end
 
       def init_from_hash(hash, &block)
         new(
-          sequence:         hash[:sequence]         || hash[:seq],
-          structure:        hash[:structure]        || hash[:str_1] || hash[:str],
-          second_structure: hash[:second_structure] || hash[:str_2],
-          comment:          hash[:comment]          || hash[:name],
+          sequence:   hash[:sequence]   || hash[:seq],
+          structures: hash[:structures] || hash[:structure] || hash[:strs] || hash[:str],
+          comment:    hash[:comment]    || hash[:name],
           &block
         )
       end
@@ -38,7 +42,7 @@ module Wrnap
         init_from_string(*array, &block)
       end
 
-      def init_from_fasta(string, &block)
+      alias_method :init_from_fa, def init_from_fasta(string, &block)
         if File.exist?(string)
           comment = File.basename(string, string.include?(?.) ? ".%s" % string.split(?.)[-1] : "")
           string  = File.read(string).chomp
@@ -46,12 +50,12 @@ module Wrnap
           
         if string.count(?>) > 1
           string.split(/>/).reject(&:empty?).map do |rna_string|
-            rna_data = rna_string.split(?\n)
+            rna_data = rna_string.split(?\n).reject(&:empty?)
             init_from_string(*rna_data[1..-1]).copy_name_from(rna_data[0])
           end.wrnap
         else
-          init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") }[0, 3], &block).tap do |rna|
-            if (line = string.split(/\n/).first).start_with?(">") && !(file_comment = line.gsub(/^>\s*/, "")).empty?
+          init_from_string(*string.split(?\n).reject { |line| line.start_with?(?>) || line.empty? }, &block).tap do |rna|
+            if (line = string.split(?\n).first).start_with?(?>) && !(file_comment = line.gsub(/^>\s*/, "")).empty?
               rna.comment = file_comment
             elsif comment
               rna.comment = comment
@@ -67,100 +71,99 @@ module Wrnap
       def init_from_self(rna, &block)
         # This happens when you call a Wrnap library function with the output of something like Wrnap::Fold.run(...).mfe
         new(
-          sequence:         rna.sequence,
-          structure:        rna.structure,
-          second_structure: rna.second_structure,
-          comment:          rna.comment,
+          sequence:   rna.sequence,
+          structures: rna.structures,
+          comment:    rna.comment,
           &block
-        )
+        ).tap do |new_rna|
+          new_rna.instance_variable_set(:@metadata, rna.metadata.clone)
+        end
+      end
+      
+      def init_from_old_rna_object(rna)
+        init_from_self(rna).tap do |new_rna|
+          new_rna.instance_variable_set(:@structures, [
+            rna.instance_variable_get(:@structure),
+            rna.instance_variable_get(:@second_structure)
+          ].compact)
+        end
       end
 
       alias_method :placeholder, :new
     end
 
-    def initialize(sequence: "", structure: "", second_structure: "", comment: "", &block)
-      @sequence, @comment, @metadata = (sequence.kind_of?(Rna) ? sequence.seq : sequence).upcase, comment, Metadata::Container.new(self)
-
-      [:structure, :second_structure].each do |structure_symbol|
-        instance_variable_set(
-          :"@#{structure_symbol}",
-          case structure_value = eval("#{structure_symbol}")
-          when :empty then empty_structure
-          when :mfe   then RNA(sequence).run(:fold).mfe_rna.structure
-          when String then structure_value
-          when Hash   then
-            if structure_value.keys.count > 1
-              Wrnap.debugger { "The following options hash has more than one key. This will probably produce unpredictable results: %s" % structure_value.inspect }
-            end
+    def initialize(sequence: "", structures: [], comment: "", &block)
+      @sequence   = (sequence.kind_of?(Rna) ? sequence.seq : sequence).upcase
+      @comment    = comment
+      @metadata   = Metadata::Container.new(self)
+      @structures = (structures ? [structures].flatten : []).each_with_index.map do |structure, i|
+        case structure
+        when :empty, :empty_str then empty_structure
+        when :mfe   then RNA(@sequence).run(:fold).mfe_rna.structure
+        when String then structure
+        when Hash   then
+          if structure.keys.count > 1
+            Wrnap.debugger { "The following options hash has more than one key. This will probably produce unpredictable results: %s" % structure.inspect }
+          end
 
-            RNA(sequence).run(*structure_value.keys, *structure_value.values).mfe_rna.structure
+          RNA(@sequence).run(*structure.keys, *structure.values).mfe_rna.structure
+        end.tap do |parsed_structure|
+          if parsed_structure.length != len
+            Wrnap.debugger { "The sequence length (%d) doesn't match the structure length at index %d (%d)" % [len, i, parsed_structure.length] }
           end
-        )
+        end
       end
 
       metadata.instance_eval(&block) if block_given?
-
-      if str && len != str.length
-        Wrnap.debugger { "The sequence length (%d) doesn't match the structure length (%d)" % [seq, str].map(&:length) }
-      end
-
-      if str_2 && str_1.length != str_2.length
-        Wrnap.debugger { "The first structure length (%d) doesn't match the second structure length (%d)" % [str_1, str_2].map(&:length) }
-      end
     end
 
-    alias :seq   :sequence
-    alias :str   :structure
-    alias :str_1 :structure
-    alias :str_2 :second_structure
-    alias :name  :comment
+    alias_method :seq,  :sequence
+    alias_method :strs, :structures
+    alias_method :name, :comment
     
-    def_delegator :@sequence, :length, :len
+    def_delegator :@sequence,   :length, :len
+    def_delegator :@structures, :first,  :structure
+    def_delegator :@structures, :first,  :str
 
     def copy_name_from(nameish)
       tap { @comment = nameish.is_a?(String) ? nameish : nameish.name }
     end
+    
+    alias_method :num_strs, def number_of_structures
+      structures.length
+    end
 
-    def empty_structure
+    alias_method :empty_str, def empty_structure
       "." * len
     end
 
-    alias :empty_str :empty_structure
-
-    def no_structure
-      self.class.init_from_string(seq, nil, nil, name)
+    alias_method :no_str, def no_structure
+      self.class.init_from_string(seq, name)
     end
 
-    alias :no_str :no_structure
-
-    def one_structure(structure_1)
-      self.class.init_from_string(seq, structure_1.is_a?(Symbol) ? send(structure_1) : structure_1, nil, name)
+    alias_method :one_str, def one_structure(structure_1)
+      self.class.init_from_string(seq, structure_1.is_a?(Symbol) ? send(structure_1) : structure_1, name)
     end
 
-    alias :one_str :one_structure
-
-    def two_structures(structure_1, structure_2)
+    alias_method :two_str, def two_structures(structure_1, structure_2)
       self.class.init_from_string(
         seq,
-        *[structure_1, structure_2].map { |argument| argument.is_a?(Symbol) ? send(argument) : argument },
+        [structure_1, structure_2].map { |argument| argument.is_a?(Symbol) ? send(argument) : argument },
         name
       )
     end
-
-    alias :two_str :two_structures
     
     def formatted_string
       [
-        (">%s" % name  if name),
-        ("%s"  % seq   if seq),
-        ("%s"  % str_1 if str_1),
-        ("%s"  % str_2 if str_2)
+        (">%s" % name if name),
+        ("%s"  % seq  if seq),
+        *structures
       ].compact.join(?\n)
     end
 
     def write_fa!(filename)
       filename.tap do |filename|
-        File.open(filename, ?w) { |file| file.write(formatted_string) }
+        File.open(filename, ?w) { |file| file.write(formatted_string + ?\n) }
       end
     end
 
@@ -180,24 +183,25 @@ module Wrnap
       other_rna.kind_of?(Wrnap::Rna) ? [seq, str_1, str_2] == [other_rna.seq, other_rna.str_1, other_rna.str_2] : super
     end
 
-    def method_missing(name, *args, &block)
-      if (name_str = "#{name}") =~ /^run_\w+$/
-        run(name_str.gsub(/^run_/, ""), *args)
-      else super end
-    end
-
     def pp
       puts(formatted_string)
     end
     
     def inspect
       "#<RNA: %s>" % [
-        ("#{seq[0, 20]   + (len          > 20 ? '... [%d]' % len          : '')}" if seq   && !seq.empty?),
-        ("#{str_1[0, 20] + (str_1.length > 20 ? ' [%d]'    % str_1.length : '')}" if str_1 && !str_1.empty?),
-        ("#{str_2[0, 20] + (str_2.length > 20 ? ' [%d]'    % str_2.length : '')}" if str_2 && !str_1.empty?),
+        ("#{seq[0, 20] + (len > 20 ? '... [%d]' % len : '')}" if seq && !seq.empty?),
+        *strs.map { |str| ("#{str[0, 20] + (str.length > 20 ? ' [%d]' % str.length : '')}" if str && !str.empty?) },
         (md.inspect unless md.nil? || md.empty?),
         (name ? name : "#{self.class.name}")
       ].compact.join(", ")
     end
+    
+    handle_methods_like(/^str(ucture)?_(\d+)$/) do |match, name, *args, &block|
+      structures[match[2].to_i - 1]
+    end
+    
+    handle_methods_like(/^run_(\w+)$/) do |match, name, *args, &block|
+      run(match[1], *args)
+    end
   end
 end

data/lib/wrnap/version.rb

@@ -1,3 +1,3 @@
 module Wrnap
-  VERSION = "1.2.0"
+  VERSION = "1.2.1"
 end

data/lib/wrnap.rb

@@ -1,12 +1,16 @@
-require "active_support/core_ext/class"
+require "active_support/core_ext"
 require "active_support/inflector"
 require "benchmark"
 require "bigdecimal"
 require "bio"
 require "bio-stockholm"
 require "entrez"
+require "meta_missing"
+require "numbers_in_words"
+require "numbers_in_words/duck_punch"
 require "parallel"
 require "rroc"
+require "scanf"
 require "set"
 require "shuffle"
 require "tempfile"

data/wrnap.gemspec

@@ -8,7 +8,7 @@ Gem::Specification.new do |spec|
   spec.version       = Wrnap::VERSION
   spec.authors       = ["Evan Senter"]
   spec.email         = ["evansenter@gmail.com"]
-  spec.summary       = %q{A comprehensive wrapper (wRNApper) for various RNA CLI programs.}
+  spec.summary       = %q{A comprehensive wrapper w(RNA)pper for various RNA CLI programs.}
   spec.description   = %q{}
   spec.homepage      = ""
   spec.license       = "MIT"
@@ -20,13 +20,17 @@ Gem::Specification.new do |spec|
 
   spec.required_ruby_version = ">= 2.0"
 
-  spec.add_development_dependency "bundler", "~> 1.6"
-  spec.add_development_dependency "rake"
+  spec.add_development_dependency "awesome_print", "~> 1.2.0"
+  spec.add_development_dependency "bundler",       "~> 1.7"
+  spec.add_development_dependency "gem-release",   "~> 0.7", ">= 0.7.3"
+  spec.add_development_dependency "rake",          "~> 10.0"
 
   spec.add_runtime_dependency "activesupport",    "~> 4.0"
   spec.add_runtime_dependency "bio",              "~> 1.4"
   spec.add_runtime_dependency "bio-stockholm",    "~> 0.0.1"
   spec.add_runtime_dependency "entrez",           "~> 0.5"
+  spec.add_runtime_dependency "meta_missing",     "~> 0.3.0"
+  spec.add_runtime_dependency "numbers_in_words", "~> 0.2.0"
   spec.add_runtime_dependency "parallel",         "~> 1.3", ">= 1.3.2"
   spec.add_runtime_dependency "rinruby",          "~> 2.0"
   spec.add_runtime_dependency "rroc",             "~> 0.1"

metadata

@@ -1,43 +1,77 @@
 --- !ruby/object:Gem::Specification
 name: wrnap
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.2.1
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-15 00:00:00.000000000 Z
+date: 2014-12-12 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: awesome_print
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.2.0
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.7'
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: gem-release
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.7.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.7.3
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement
@@ -94,6 +128,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.5'
+- !ruby/object:Gem::Dependency
+  name: meta_missing
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+- !ruby/object:Gem::Dependency
+  name: numbers_in_words
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
 - !ruby/object:Gem::Dependency
   name: parallel
   requirement: !ruby/object:Gem::Requirement
@@ -272,9 +334,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.2
+rubygems_version: 2.4.5
 signing_key: 
 specification_version: 4
-summary: A comprehensive wrapper (wRNApper) for various RNA CLI programs.
+summary: A comprehensive wrapper w(RNA)pper for various RNA CLI programs.
 test_files: []
-has_rdoc: