wrnap 1.0.1 → 1.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5a49216040e651785e22f2fe010a08ad6ace0800
-  data.tar.gz: beb5164b299e498a0a0c1d59ca579efb723aef46
+  metadata.gz: b2cc53a30fd53e8dc635b9a6f0e6b9dfc985eefb
+  data.tar.gz: ce9692b9164e77fac7b6d4e56ed6398500c19e71
 SHA512:
-  metadata.gz: b4262912d96fa147269069032324e0319cc8deb5391dd56376acdea9165c9cc48ddf3d3755c221d9bdc1d503d6bda8840962b5437dc7522a1244571ed089d017
-  data.tar.gz: 29c9eb3b9c20d32c6cdda08a6629fbf5917bfb482a3b76e2ac1f9150ecc54c799320789387a9d97fc4f8b35810fc4877d0e1667fc3166834a548b7f43d0f06eb
+  metadata.gz: 6e5c9b208ddb20f3d9377a40bfa6e5467a35c9012ddd0a0e38bcb47f082de147bd82df8ef7040a9dad2910f87f6bcc18df79b0f187a142f5ba99afa6bcc76d17
+  data.tar.gz: cf74fe53fde6cbdf70a7430d6dee2e56cbbcd12ad64b9a9e6c11a68e279b7a46657ffd2fe1b5d5ed9d813e223016f27479a638b72e8f05537ed1f0762cb22f92

data/lib/wrnap/etl/infernal.rb

@@ -7,7 +7,7 @@ module Wrnap
       LOCAL_END     = /\*\[\s*\d+\s*\]\*/
 
       class << self
-        def parse_file(file)
+        def load_all(file)
           output = File.exist?(file) ? File.read(file) : file
 
           if output =~ /No hits detected that satisfy reporting thresholds/
@@ -17,7 +17,7 @@ module Wrnap
               gsub(/^(.*\n)*Hit alignments:\n/, "").
               gsub(/Internal CM pipeline statistics summary:\n(.*\n)*$/, "").
               strip.split(?\n).reject(&:empty?).each_slice(10).map { |lines| parse_hit(lines.join(?\n)) }.compact
-          end
+          end.wrnap
         end
 
         def parse_hit(output)

data/lib/wrnap/etl/stockholm.rb

@@ -4,10 +4,21 @@ module Wrnap
       class << self
         def load_all(file)
           entries   = Bio::Stockholm::Reader.parse_from_file(file)[0]
-          sequences = entries.records.map(&:last).map(&:sequence)
-          structure = dot_bracket_from_stockholm(entries.gc_features["SS_cons"])
+          structure = consensus_structure_from_file(file)
 
-          sequences.map { |sequence| fit_structure_to_sequence(sequence, structure) }
+          entries.records.map do |label, record| 
+            fit_structure_to_sequence(record.sequence, structure).tap do |rna| 
+              rna.comment = if !record.gs_features.nil? && record.gs_features.is_a?(Hash)
+                record.gs_features["AC"].split(/[\/-]/).join(" ")
+              else
+                label.split(/[\/-]/).join(" ")
+              end
+            end
+          end.wrnap
+        end
+        
+        def consensus_structure_from_file(file)
+          dot_bracket_from_stockholm(Bio::Stockholm::Reader.parse_from_file(file)[0].gc_features["SS_cons"])
         end
 
         def dot_bracket_from_stockholm(structure)

data/lib/wrnap/global/entrez.rb

@@ -19,16 +19,18 @@ module Wrnap
         def sequence_from_entrez(id, position, window)
           Wrnap.debugger { "Retrieving sequence from Entrez: using nuccore DB (id: #{id}, seq_start: #{position + window.min}, seq_stop: #{position + window.max})" }
           Wrnap.debugger { "> True starting position: #{position} with window #{window.min} to #{window.max}" }
-
+          
           fasta = ::Entrez.EFetch("nuccore", {
             id:        id,
             seq_start: position + window.min,
             seq_stop:  position + window.max,
             retmode:   :fasta,
             rettype:   :text
-          }).response.body
+          })
+          
+          Wrnap.debugger { fasta }
 
-          Bio::FastaFormat.new(fasta)
+          Bio::FastaFormat.new(fasta.response.body)
         end
       end
     end

data/lib/wrnap/global/runner.rb

@@ -10,6 +10,10 @@ module Wrnap
         def exec_exists?(name)
           !%x[which RNA#{name.to_s.downcase}].empty? || !%x[which #{name.to_s.downcase}].empty?
         end
+        
+        def exec_name
+          executable_name.respond_to?(:call) ? executable_name[self] : executable_name
+        end
 
         def run(*data)
           flags = data.length > 1 && data.last.is_a?(Hash) ? data.pop : {}
@@ -40,13 +44,23 @@ module Wrnap
         end
 
         def pre_run_check
-          if %x[which #{exec_name}].empty?
+          valid_to_run = if self.class.instance_variable_get(:@pre_run_checked)
+            self.class.instance_variable_get(:@valid_to_run)
+          else
+            Wrnap.debugger { "Checking existence of executable %s." % exec_name }
+            self.class.module_eval do
+              @pre_run_checked = true
+              @valid_to_run    = !%x[which #{exec_name}].empty?
+            end
+          end
+          
+          unless valid_to_run
             raise RuntimeError.new("#{exec_name} is not defined on this machine")
           end
         end
 
         def exec_name
-          executable_name.respond_to?(:call) ? executable_name[self] : executable_name
+          self.class.exec_name
         end
 
         def recursively_merge_flags(flags)

data/lib/wrnap/graphing/r.rb

@@ -2,10 +2,10 @@ module Wrnap
   module Graphing
     module R
       class << self
-        def graph(&block)
+        def graph(width: 8, height: 6, &block)
           if const_defined?(:RinRuby)
             begin
-              (yield (r_instance = RinRuby.new(false))).tap { r_instance.close }
+              generate_graph(r_instance = RinRuby.new(false), width, height, &block).tap { r_instance.close }
             rescue RuntimeError => e
               raise unless e.message == "Unsupported data type on R's end"
             end
@@ -23,11 +23,6 @@ module Wrnap
           y_range  = Range.new(y_points.map(&:min).min.floor, y_points.map(&:max).max.ceil)
 
           graph do |r|
-            r.eval("%s('%s', 6, 6)" % [
-              writing_file?(filename) ? filetype(filename) : "quartz",
-              writing_file?(filename) ? filename : "Graph",
-            ])
-
             r.assign("legend.titles", data.each_with_index.map { |hash, index| hash[:legend] || "Line #{index + 1}" })
             r.eval("line.colors <- rainbow(%d)" % data.size)
             r.eval("plot(0, 0, type = 'n', cex = .75, cex.axis = .9, xlab = '', ylab = '', xlim = c(%d, %d), ylim = c(%d, %d))" % [
@@ -73,8 +68,6 @@ module Wrnap
                 )
               STR
             end
-
-            r.eval("dev.off()") if writing_file?(filename)
           end
         end
 
@@ -115,7 +108,6 @@ module Wrnap
             end
           end
 
-
           overlay(
             formatted_data,
             title:    title,
@@ -135,11 +127,6 @@ module Wrnap
             r.assign("histogram.data", data)
             r.assign("histogram.breaks", breaks)
 
-            r.eval("%s('%s', 6, 6)" % [
-              writing_file?(filename) ? filetype(filename) : "quartz",
-              writing_file?(filename) ? filename : "Graph",
-            ])
-
             r.eval <<-STR
               hist(
                 histogram.data,
@@ -154,8 +141,6 @@ module Wrnap
             STR
 
             r.eval("abline(v = #{x_arrow}, lty = 'dashed')") if x_arrow
-
-            r.eval("dev.off()") if writing_file?(filename)
           end
         end
 
@@ -179,26 +164,22 @@ module Wrnap
                 x      = matrix.x,
                 index1 = F
                 )
+                
+                filtered.values <- Filter(function(i) { is.finite(i) & i != 0 }, matrix.x)
+                print(apply(as.matrix(matrix.data), 2, rev))
+                print(c(sort(filtered.values)[2], max(filtered.values)))
+
+                image(
+                  x    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])),
+                  y    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])),
+                  z    = as.matrix(matrix.data),
+                  col  = rev(heat.colors(#{num_colors})),
+                  zlim = #{forced_square ? "c(sort(filtered.values)[2], max(filtered.values))" : "c(min(filtered.values), max(filtered.values))"},
+                  xlab = "#{x_label} (1-indexed)",
+                  ylab = "#{y_label} (1-indexed)"
+                )
+                title(#{expressionify(title || "Matrix Heatmap")})
               STR
-
-              generate_graph("Heatmap") do
-                <<-STR
-                  filtered.values <- Filter(function(i) { is.finite(i) & i != 0 }, matrix.x)
-                  print(apply(as.matrix(matrix.data), 2, rev))
-                  print(c(sort(filtered.values)[2], max(filtered.values)))
-
-                  image(
-                    x    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])),
-                    y    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])),
-                    z    = as.matrix(matrix.data),
-                    col  = rev(heat.colors(#{num_colors})),
-                    zlim = #{forced_square ? "c(sort(filtered.values)[2], max(filtered.values))" : "c(min(filtered.values), max(filtered.values))"},
-                    xlab = "#{x_label} (1-indexed)",
-                    ylab = "#{y_label} (1-indexed)"
-                  )
-                  title(#{expressionify(title || "Matrix Heatmap")})
-                STR
-              end
             else
               puts "Please install the Matrix package for R before using this function."
             end
@@ -207,15 +188,17 @@ module Wrnap
 
         private
 
-        def generate_graph(window_title = "ViennaRNA Graph in R", &block)
-          r, filename = block.binding.eval("[r, filename]")
+        def generate_graph(r, width, height, &block)
+          filename = block.binding.eval("filename")
 
-          r.eval("%s('%s', 6, 6)" % [
+          r.eval("%s('%s', %d, %d)" % [
             writing_file?(filename) ? filetype(filename) : "quartz",
             writing_file?(filename) ? filename : "Graph",
+            width,
+            height
           ])
 
-          r.eval(yield)
+          yield r
 
           r.eval("dev.off()") if writing_file?(filename)
         end

data/lib/wrnap/package/base.rb

@@ -10,7 +10,7 @@ module Wrnap
       include Wrnap::Global::Yaml
 
       class_attribute :executable_name
-      self.executable_name = ->(context) { "RNA#{context.class.name.split('::').last.underscore}" }
+      self.executable_name = ->(context) { "RNA#{context.name.split('::').last.underscore}" }
 
       class_attribute :call_with
       self.call_with = [:seq]

data/lib/wrnap/package/varna.rb

@@ -15,7 +15,7 @@ module Wrnap
       self.quote_flag_params = %w|sequenceDBN structureDBN title|
 
       def run_command(flags)
-        "java fr.orsay.lri.varna.applications.VARNAcmd %s" % stringify_flags(flags)
+        "java -Djava.awt.headless=true fr.orsay.lri.varna.applications.VARNAcmd %s" % stringify_flags(flags)
       end
     end
   end

data/lib/wrnap/package/xbor.rb

@@ -5,7 +5,7 @@ module Wrnap
         E: "/usr/local/bin/rna_turner2004.par"
       }
     
-      self.executable_name = ->(context) { context.class.name.demodulize.gsub(/^([A-Z].*)bor$/) { |match| $1.upcase + "bor" } }
+      self.executable_name = ->(context) { context.name.demodulize.gsub(/^([A-Z].*)bor$/) { |match| $1.upcase + "bor" } }
     
       def run_command(flags)
         file = Tempfile.new("rna")

data/lib/wrnap/rna/box.rb

@@ -9,13 +9,19 @@ module Wrnap
 
       class << self
         def load_all(pattern = "*.fa", &block)
-          new(Dir[File.directory?(pattern) ? pattern + "/*.fa" : pattern].map { |file| RNA.from_fasta(file, &block) })
+          new(Dir[File.directory?(pattern) ? pattern + "/*.fa" : pattern].inject([]) { |array, file| array + RNA.from_fasta(file, &block).rnas })
         end
       end
 
       def initialize(rnas)
         @rnas = rnas.kind_of?(Array) ? rnas : [rnas]
       end
+      
+      def write_fa!(filename)
+        filename.tap do |filename|
+          File.open(filename, ?w) { |file| file.write(rnas.map(&:formatted_string).join(?\n) + ?\n) }
+        end
+      end
 
       def pp
         rnas.each(&:pp) and nil
@@ -25,15 +31,27 @@ module Wrnap
         self.class.new(rnas + (arrayish.is_a?(Box) ? arrayish.rnas : arrayish))
       end
 
-      def_delegators :@rnas, *%i|size length [] []= <<|
+      def_delegators :@rnas, *%i|size length first last [] []= <<|
 
       def each(&block)
+        return enum_for(:each) unless block_given?
         rnas.each(&block)
       end
+      
+      def run_in_parallel(method, *args)
+        Wrnap.debug, debug_status = false, Wrnap.debug
+        Parallel.map(self, progress: "Calling %s on %d RNAs" % [method, rnas.size]) { |rna| rna.send(method, *args) }.tap { Wrnap.debug = debug_status }
+      end
 
       def kind_of?(klass)
         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
+      end
 
       def inspect
         "#<Wrnap::Rna::Box with %d RNAs>" % rnas.size

data/lib/wrnap/rna/constraints.rb

@@ -9,6 +9,10 @@ module Wrnap
         def constraint_mask
           md[:constraint_mask]
         end
+        
+        def show_constraints(&block)
+          ConstraintBox.new(metadata.__rna__).tap { |box| box.instance_eval(&block) }.to_s
+        end
 
         def build_constraints(&block)
           meta_rna do |metadata|
@@ -23,6 +27,10 @@ module Wrnap
         def initialize(rna)
           @rna, @constraints = rna, []
         end
+        
+        def n
+          rna.len - 1
+        end
 
         def between(i, j)
           Loop.new(i, j)
@@ -32,10 +40,25 @@ module Wrnap
           between(i + 1, j - 1)
         end
         
+        def start_to(i)
+          between(0, i)
+        end
+        
+        def end_to(i)
+          between(i, n)
+        end
+        
+        def freeze(mask_object)
+          force mask_object
+          prohibit mask_object.unpaired_regions
+        end
+        
         def mask!(mask_object, *args)
           case mask_object
-          when Helix then mask_helix!(mask_object, *args)
-          when Loop  then mask_loop!(mask_object, symbol: args[0][:symbol])
+          when TreeStem then mask_object.preorder_traversal { |node| mask!(node.content, *args) }
+          when Array    then mask_object.map { |node| mask!(node, *args) }
+          when Helix    then mask_helix!(mask_object, *args)
+          when Loop     then mask_loop!(mask_object, symbol: args[0][:symbol])
           end
         end
 

data/lib/wrnap/rna/context.rb

@@ -1,14 +1,16 @@
 module Wrnap
   class Rna
     class Context < Rna
+      extend Forwardable
+      
       attr_reader :accession, :from, :to, :coord_options
 
       class << self
         def init_from_entrez(accession, from, to, options = {}, &block)
           new(
             accession: accession,
-            from:      from,
-            to:        to,
+            from:      from.to_i,
+            to:        to.to_i,
             options:   options,
             &block
           )
@@ -18,8 +20,8 @@ module Wrnap
           new(
             sequence:  sequence,
             accession: accession,
-            from:      from,
-            to:        to,
+            from:      from.to_i,
+            to:        to.to_i,
             options:   options,
             &block
           )
@@ -102,6 +104,8 @@ module Wrnap
       end
 
       alias :seq :sequence
+      
+      def_delegator :@raw_sequence, :length, :len
 
       def extend!(coord_options = {})
         self.class.init_from_entrez(accession, from, to, coords: coord_options)
@@ -126,14 +130,22 @@ module Wrnap
           range
         end
       end
-
+      
       def identifier
-        "%s %d %s %d" % [accession, from, plus_strand? ? ?+ : ?-, to]
+        "%s %d %s %d" % [accession, seq_from, plus_strand? ? ?+ : ?-, seq_to]
+      end
+      
+      def _id
+        identifier.gsub(/[^A-Z0-9]/, ?_).gsub(/__+/, ?_)
       end
 
       def inspect
-        super.gsub(/((\w(::)?)+)>$/) { |_| "%s %s>" % [identifier, $1] }
+        if super.match(/Wrnap::(\w+(::)?)+>$/)
+          super.sub(/([\w:]+)>$/) { |_| "%s %s>" % [identifier, $1] }
+        else
+          super
+        end
       end
     end
   end
-end
+end

data/lib/wrnap/rna/extensions.rb

@@ -39,8 +39,53 @@ module Wrnap
       end
 
       module InstanceMethods
+        def hamming_distance(other_rna)
+          raise "The two sequences are not the same length" unless len == other_rna.len
+          
+          [seq, other_rna.seq].map(&:each_char).map(&:to_a).transpose.select { |array| array.uniq.size > 1 }.count
+        end
+        
+        def local_structural_shuffle(dishuffle: false)
+          sequence       = " " * len
+          loops, helices = loops_and_helices
+        
+          loops.each { |loop| sequence[loop.i..loop.j] = Shuffle.new(loop.in(seq)).send(dishuffle ? :dishuffle : :shuffle) }
+          helices.each do |helix|
+            left_stem, right_stem = if dishuffle
+              Shuffle.new(helix.in(seq)).dishuffle
+            else
+              Shuffle.new(helix.in(seq)).shuffle.map { |array| rand(2).zero? ? array : array.reverse }
+            end.transpose.map(&:join)
+            
+            sequence[helix.i..helix.k] = left_stem
+            sequence[helix.l..helix.j] = right_stem.reverse
+          end
+          
+          Rna.init_from_string(sequence, str)
+        end
+        
+        def local_structural_dishuffle
+          local_structural_shuffle(dishuffle: true)
+        end
+        
+        def global_structural_shuffle
+          sequence         = " " * len
+          loops, helices   = loops_and_helices
+          shuffled_loops   = Shuffle.new(loops.map { |loop| loop.in(seq) }.join.split(//)).shuffle
+          shuffled_helices = helices.map { |helix| helix.in(seq) }.inject(&:+).shuffle.map { |array| rand(2).zero? ? array : array.reverse }
+        
+          loops.each { |loop| sequence[loop.i..loop.j] = shuffled_loops.shift(loop.length).join }
+          helices.each do |helix|
+            left_stem, right_stem      = shuffled_helices.shift(helix.length).transpose.map(&:join)
+            sequence[helix.i..helix.k] = left_stem
+            sequence[helix.l..helix.j] = right_stem.reverse
+          end
+          
+          Rna.init_from_string(sequence, str)
+        end
+        
         def dishuffle
-          self.class.shuffle(sequence, 2)
+          Rna.init_from_string(self.class.shuffle(sequence, 2))
         end
 
         def gc_content
@@ -56,6 +101,33 @@ module Wrnap
         def max_bp_distance(structure)
           base_pairs(structure).count + ((structure.length - 3) / 2.0).floor
         end
+        
+        def loops_and_helices(structure)
+          [loop_regions(structure), collapsed_helices(structure, lonely_bp: true)]
+        end
+        
+        def loop_regions(structure)
+          [structure.split(//), (0...structure.length).to_a].transpose.select { |char, _| char == ?. }.inject([]) do |array, (_, index)|
+            array.tap do
+              matching_loop = array.map(&:last).each_with_index.find { |end_of_loop, _| end_of_loop + 1 == index }
+              matching_loop ? array[matching_loop[-1]][-1] += 1 : array << [index, index]
+            end
+          end.map { |loop_indices| Loop.new(*loop_indices) }
+        end
+        
+        def helices(structure)
+          unless (array = base_pairs(structure).sort_by(&:first).map(&:to_a)).empty?
+            array[1..-1].inject([[array.first]]) do |bins, (i, j)|
+              bins.tap { bins[-1][-1] == [i - 1, j + 1] ? bins[-1] << [i, j] : bins << [[i, j]] }
+            end
+          else
+            []
+          end
+        end
+
+        def collapsed_helices(structure, lonely_bp: false)
+          helices(structure).map { |((i, j), *rest)| Helix.new(i, j, rest.length + 1) }.select { |helix| lonely_bp ? helix : helix.length > 1 }
+        end
 
         def base_pairs(structure)
           get_pairings(structure).each_with_index.inject(Set.new) do |set, (j, i)|

data/lib/wrnap/rna/motifs.rb

@@ -1,23 +1,5 @@
 module Wrnap
-  class Rna
-    module Motifs
-      def helices
-        array = base_pairs.sort_by(&:first).map(&:to_a)
-
-        unless array.empty?
-          array[1..-1].inject([[array.first]]) do |bins, (i, j)|
-            bins.tap { bins[-1][-1] == [i - 1, j + 1] ? bins[-1] << [i, j] : bins << [[i, j]] }
-          end
-        else
-          []
-        end
-      end
-
-      def collapsed_helices(lonely_bp: false)
-        helices.map { |((i, j), *rest)| Helix.new(i, j, rest.length + 1) }.select { |helix| lonely_bp ? helix : helix.length > 1 }
-      end
-    end
-
+  class Rna    
     class Helix
       attr_reader :i, :j, :length
 
@@ -28,9 +10,26 @@ module Wrnap
       def k; i + length - 1; end
       def l; j - length + 1; end
       
+      def in(sequence)
+        (0...length).map do |stem_position|
+          [sequence[i + stem_position], sequence[j - stem_position]]
+        end
+      end
+      
       def to_loops
         [Loop.new(i, k), Loop.new(l, j)]
       end
+      
+      def apply!(structure)
+        structure.tap do
+          structure[i, length] = ?( * length
+          structure[l, length] = ?) * length
+        end
+      end
+      
+      def merge!(helix)
+        @length = helix.k - i + 1
+      end
 
       def reindex!(rna)
         tap do
@@ -45,7 +44,7 @@ module Wrnap
       end
 
       def name
-        "(%d..%d, %d..%d)" % [i, k, l, j]
+        "(%d..%d, %d..%d [%d])" % [i, k, l, j, length]
       end
 
       def inspect
@@ -60,8 +59,16 @@ module Wrnap
         @i, @j = i, j
       end
       
+      def in(sequence)
+        sequence[i..j]
+      end
+      
+      def length
+        j - i + 1
+      end
+      
       def name
-        "(%d, %d)" % [i, j]
+        "(%d, %d [%d])" % [i, j, length]
       end
       
       def inspect

data/lib/wrnap/rna/tree.rb

@@ -14,19 +14,84 @@ module Wrnap
       extend Forwardable
       include Enumerable
 
-      STEM_NOTATION_REGEX = /^p((\d+_)*(\d+))(_?([ijkl]))?$/
+      STEM_NOTATION_REGEX = /^[pt]_?(\d+_)*\d+(_?[ijkl])?$/
 
-      def_delegators :@content, :i, :j
+      def_delegators :@content, :i, :j, :k, :l
       def_delegator  :@content, :length, :stem_length
+      
+      def unpaired_regions
+        Wrnap.debugger { "Collecting unpaired regions for %s" % [root.content.name] }
+        
+        postorder_traversal.inject([]) do |array, node|
+          array.tap do
+            if node.is_leaf?
+              array << Loop.new(node.k + 1, node.l - 1)
+            end
+            
+            if node != self
+              if node.is_only_child?
+                Wrnap.debugger { "Interior node: %s, parent: %s" % [node.content.inspect, node.parent.content.inspect] }
+          
+                if node.i - node.parent.k > 0
+                  Wrnap.debugger { "Left bulge." }
+                  array << Loop.new(node.parent.k + 1, node.i - 1)
+                end
+          
+                if node.parent.l - node.j > 0
+                  Wrnap.debugger { "Right bulge." }
+                  array << Loop.new(node.j + 1, node.parent.l - 1)
+                end
+              else
+                node_index = node.parent.children.each_with_index.find { |child, _| child == node }.last
+              
+                if node.is_last_sibling?
+                  Wrnap.debugger { "Leaf node, last child: %s" % node.content.inspect }
+                  array << Loop.new(node.j + 1, node.parent.l - 1)
+                else
+                  if node.is_first_sibling?
+                    Wrnap.debugger { "Leaf node, first child: %s" % node.content.inspect }
+                    array << Loop.new(node.parent.k + 1, node.i - 1) 
+                  end
+                
+                  Wrnap.debugger { "Connecting node, middle child: %s" % node.content.inspect }
+                  alexa = node.siblings[node_index]
+                  array << Loop.new(node.j + 1, alexa.i - 1)
+                end
+              end
+            end            
+          end
+        end
+      end
+      
+      def detached_copy
+        self.class.new(@name, @content ? @content.clone : nil)
+      end
+      
+      def preorder_traversal(&block)
+        return enum_for(:preorder_traversal) unless block_given?
+        yield self
+        children.map { |child| child.preorder_traversal(&block) }
+      end
+      
+      def postorder_traversal(&block)
+        return enum_for(:postorder_traversal) unless block_given?
+        children.each { |child| child.postorder_traversal(&block) }
+        yield self
+      end
 
       def method_missing(name, *args, &block)
-        if name.to_s =~ STEM_NOTATION_REGEX
-          if $2 && child = children[$2.to_i - 1]
-            child.send("p%s" % name.to_s.gsub(/^p\d+_/, ""))
-          elsif child = children[$1.to_i - 1]
-            $5 ? child.content.send($5) : child.content
-          else
-            nil
+        if (method_name = name.to_s) =~ STEM_NOTATION_REGEX
+          call_type   = method_name[0]
+          indices     = method_name.gsub(/\D+/, ?_).split(?_).reject(&:empty?).map(&:to_i)
+          helix_index = method_name.match(/([ijkl])$/) ? $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
           end
         else super end
       end
@@ -85,14 +150,35 @@ module Wrnap
       def coalesce!
         tap { merge_interior_loops! }
       end
+      
+      def fuse
+        self.class.new(rna, root.dup).tap { |tree| tree.extend_interior_loops! }
+      end
 
+      def fuse!
+        tap { extend_interior_loops! }
+      end
+  
+      def extend_interior_loops!
+        handle_interior_loops! do |node, child|
+          node.content.merge!(child.content)
+          child.remove_from_parent!
+          child.children.each { |grandchild| node.add(grandchild) }
+        end
+      end
+  
       def merge_interior_loops!
+        handle_interior_loops! do |node, child|
+          node.parent.add(child)
+          node.remove_from_parent!
+        end
+      end
+      
+      def handle_interior_loops!(&block)
         root.tap do
-          self.class.postorder_traversal(root) do |node|
-            if node.children.count == 1 && !node.is_root?
-              child = node.children.first
-              node.parent.add(child)
-              node.remove_from_parent!
+          root.postorder_traversal do |node|
+            if node.children.count == 1 && !node.is_root?              
+              yield(node, node.children.first)
             end
           end
           
@@ -119,18 +205,6 @@ module Wrnap
           root.send(name, *args, &block)
         else super end
       end
-
-      class << self
-        def preorder_traversal(node, &block)
-          node.children.map { |child| preorder_traversal(child, &block) }
-          yield node
-        end
-
-        def postorder_traversal(node, &block)
-          node.children.map { |child| postorder_traversal(child, &block) }
-          yield node
-        end
-      end
     end
   end
 end

data/lib/wrnap/rna.rb

@@ -5,7 +5,6 @@ module Wrnap
     include Wrnap::Rna::Extensions
     include Wrnap::Rna::Wrnapper
     include Wrnap::Rna::Metadata
-    include Wrnap::Rna::Motifs
     include Wrnap::Rna::TreeFunctions
     include Wrnap::Rna::Constraints
 
@@ -44,12 +43,19 @@ module Wrnap
           comment = File.basename(string, string.include?(?.) ? ".%s" % string.split(?.)[-1] : "")
           string  = File.read(string).chomp
         end
-
-        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?
-            rna.comment = file_comment
-          elsif comment
-            rna.comment = comment
+          
+        if string.count(?>) > 1
+          string.split(/>/).reject(&:empty?).map do |rna_string|
+            rna_data = rna_string.split(?\n)
+            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?
+              rna.comment = file_comment
+            elsif comment
+              rna.comment = comment
+            end
           end
         end
       end
@@ -62,8 +68,8 @@ module Wrnap
         # This happens when you call a Wrnap library function with the output of something like Wrnap::Fold.run(...).mfe
         new(
           sequence:         rna.sequence,
-          strucutre:        rna.structure,
-          second_strucutre: rna.second_structure,
+          structure:        rna.structure,
+          second_structure: rna.second_structure,
           comment:          rna.comment,
           &block
         )
@@ -111,8 +117,8 @@ module Wrnap
     
     def_delegator :@sequence, :length, :len
 
-    def copy_name_from(rna)
-      tap { @comment = rna.name }
+    def copy_name_from(nameish)
+      tap { @comment = nameish.is_a?(String) ? nameish : nameish.name }
     end
 
     def empty_structure
@@ -142,15 +148,19 @@ module Wrnap
     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)
+      ].compact.join(?\n)
+    end
 
     def write_fa!(filename)
       filename.tap do |filename|
-        File.open(filename, ?w) do |file|
-          file.write("> %s\n" % name) if name
-          file.write("%s\n" % seq)    if seq
-          file.write("%s\n" % str_1)  if str_1
-          file.write("%s\n" % str_2)  if str_2
-        end
+        File.open(filename, ?w) { |file| file.write(formatted_string) }
       end
     end
 
@@ -177,18 +187,14 @@ module Wrnap
     end
 
     def pp
-      puts("> %s" % name)       if name
-      puts("%s" % seq)          if seq
-      puts("%s" % str_1)        if str_1
-      puts("%s" % str_2)        if str_2
-      puts("%s" % meta.inspect) if meta
+      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]'    % len : '')}" if str_1 && !str_1.empty?),
-        ("#{str_2[0, 20] + (str_2.length > 20 ? ' [%d]'    % len : '')}" if str_2 && !str_1.empty?),
+        ("#{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?),
         (md.inspect unless md.nil? || md.empty?),
         (name ? name : "#{self.class.name}")
       ].compact.join(", ")

data/lib/wrnap/version.rb

@@ -1,3 +1,3 @@
 module Wrnap
-  VERSION = "1.0.1"
+  VERSION = "1.2.0"
 end

data/lib/wrnap.rb

@@ -1,16 +1,17 @@
-require "yaml"
+require "active_support/core_ext/class"
+require "active_support/inflector"
 require "benchmark"
-require "set"
-require "tree"
-require "shuffle"
-require "tempfile"
 require "bigdecimal"
-require "rroc"
 require "bio"
 require "bio-stockholm"
 require "entrez"
-require "active_support/inflector"
-require "active_support/core_ext/class"
+require "parallel"
+require "rroc"
+require "set"
+require "shuffle"
+require "tempfile"
+require "tree"
+require "yaml"
 
 unless %x[which R].empty?
   require "rinruby"

data/wrnap.gemspec

@@ -23,12 +23,14 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "bundler", "~> 1.6"
   spec.add_development_dependency "rake"
 
-  spec.add_runtime_dependency "activesupport", "~> 4.0"
-  spec.add_runtime_dependency "shuffle",       "~> 0.1"
-  spec.add_runtime_dependency "rinruby",       "~> 2.0"
-  spec.add_runtime_dependency "rroc",          "~> 0.1"
-  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 "rubytree",      "~> 0.9"
+  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 "parallel",         "~> 1.3", ">= 1.3.2"
+  spec.add_runtime_dependency "rinruby",          "~> 2.0"
+  spec.add_runtime_dependency "rroc",             "~> 0.1"
+  spec.add_runtime_dependency "ruby-progressbar", "~> 1.5", ">= 1.5.1"
+  spec.add_runtime_dependency "rubytree",         "~> 0.9"
+  spec.add_runtime_dependency "shuffle",          "~> 1.0", ">= 1.0.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: wrnap
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.2.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-31 00:00:00.000000000 Z
+date: 2014-10-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -53,89 +53,115 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '4.0'
 - !ruby/object:Gem::Dependency
-  name: shuffle
+  name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: '1.4'
 - !ruby/object:Gem::Dependency
-  name: rinruby
+  name: bio-stockholm
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: 0.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.0'
+        version: 0.0.1
 - !ruby/object:Gem::Dependency
-  name: rroc
+  name: entrez
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: '0.5'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: '0.5'
 - !ruby/object:Gem::Dependency
-  name: bio
+  name: parallel
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '1.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '1.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.2
 - !ruby/object:Gem::Dependency
-  name: bio-stockholm
+  name: rinruby
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.0.1
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.0.1
+        version: '2.0'
 - !ruby/object:Gem::Dependency
-  name: entrez
+  name: rroc
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: ruby-progressbar
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.5'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.5.1
 - !ruby/object:Gem::Dependency
   name: rubytree
   requirement: !ruby/object:Gem::Requirement
@@ -150,6 +176,26 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.9'
+- !ruby/object:Gem::Dependency
+  name: shuffle
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.1
 description: ''
 email:
 - evansenter@gmail.com
@@ -226,8 +272,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.2
 signing_key: 
 specification_version: 4
 summary: A comprehensive wrapper (wRNApper) for various RNA CLI programs.
 test_files: []
+has_rdoc: