wrnap 1.2.1 → 1.2.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f2efcb65abde80f14ce6f0e5eba3d5438b23ba33
-  data.tar.gz: 6c7873c5b0936b137a7f0f957f4853bcdc48d345
+  metadata.gz: d7152b75ccf68c5de1ca50f9f0d45e226315b19e
+  data.tar.gz: f10da874182ca44bd751447d7982123554a98506
 SHA512:
-  metadata.gz: aa223b71c6b69f3207ebf76b4b34b90a73d4686293adc10579936d3ac609247648ff62dd1f4cf529ac6be9b8fa28010151c673c39c6d0ef4040ecacc07a3875f
-  data.tar.gz: 3808f6f38a0c3a9a5877e3d829afab5fe11766d31dd55a1091207a774dfa31b87d3b4376a1baaf1adc15c396d6cc85f403e4af30eb031a5f5f83964ee5bf4b88
+  metadata.gz: f8f4c460003509e340cc47681f6b6a3cd71ec90edf2a612bfe7fd2fb4248dfcce4c73cd274eec3b8350904380410542bcaa2cf82cf7e361019e77829bfc7bf73
+  data.tar.gz: 80ca9ab389a258371c9ec97c90a7b1ce64c3976155eae2a9d0fac31eeceece4b0e341ba45c5ed447ddb5a55ef9d8c5f5fae52e3d8c7a41dd9d27e45631b3498b

data/lib/wrnap/rna.rb

@@ -68,27 +68,6 @@ module Wrnap
         Context.init_from_entrez(*context, coords: coords, rna: rna, &block)
       end
 
-      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,
-          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
 

data/lib/wrnap/rna/box.rb

@@ -7,6 +7,7 @@ module Wrnap
       include Wrnap::Global::Yaml
 
       attr_reader :rnas
+      attr_accessor :name
 
       class << self
         def load_all(pattern = "*.fa", &block)
@@ -17,8 +18,8 @@ module Wrnap
         end
       end
 
-      def initialize(rnas)
-        @rnas = rnas.kind_of?(Array) ? rnas : [rnas]
+      def initialize(rnas, name = "")
+        @rnas, @name = rnas.kind_of?(Array) ? rnas : [rnas], name
       end
       
       def write_fa!(filename)
@@ -56,7 +57,7 @@ module Wrnap
       end
 
       def inspect
-        "#<Wrnap::Rna::Box with %d RNAs>" % rnas.size
+        ("#<Wrnap::Rna::Box %s with %d RNAs>" % [name, rnas.size]).gsub(/\s\s+/, " ")
       end
     end
   end

data/lib/wrnap/rna/tree.rb

@@ -69,6 +69,8 @@ module Wrnap
       end
       
       def detached_copy
+        # The implementation of this in RubyTree explicitly returns a new Tree::TreeNode instance rather than self.class.new, so we
+        # maintain ducktyping by intercepting the method.
         self.class.new(@name, @content ? @content.clone : nil)
       end
       
@@ -148,6 +150,23 @@ module Wrnap
           subtree << node
         end
       end
+      
+      # RNA.from_fa("xpt.fa").trunk.pp
+      # * root
+      # |---+ (5..12, 66..73 [8])
+      # |    |---> (18..22, 30..34 [5])
+      # |    +---> (45..50, 58..63 [6])
+      # |---+ (75..78, 102..105 [4])     <-
+      # |    +---> (80..86, 95..101 [7]) <-
+      # +---> (112..125, 133..146 [14])
+      #
+      # RNA.from_fa("xpt.fa").trunk.coalesce.pp
+      # * root
+      # |---+ (5..12, 66..73 [8])
+      # |    |---> (18..22, 30..34 [5])
+      # |    +---> (45..50, 58..63 [6])
+      # |---> (80..86, 95..101 [7])      <-
+      # +---> (112..125, 133..146 [14])
 
       def coalesce
         self.class.new(rna, root.clone).tap { |tree| tree.merge_interior_loops! }
@@ -157,6 +176,22 @@ module Wrnap
         tap { merge_interior_loops! }
       end
       
+      # RNA.from_fa("xpt.fa").trunk.pp
+      # * root
+      # |---+ (5..12, 66..73 [8])
+      # |    |---> (18..22, 30..34 [5])
+      # |    +---> (45..50, 58..63 [6])
+      # |---+ (75..78, 102..105 [4])     <-
+      # |    +---> (80..86, 95..101 [7]) <-
+      # +---> (112..125, 133..146 [14])
+      #
+      # RNA.from_fa("xpt.fa").trunk.fuse.pp
+      # * root
+      # |---+ (5..12, 66..73 [8])
+      # |    |---> (18..22, 30..34 [5])
+      # |    +---> (45..50, 58..63 [6])
+      # |---> (75..86, 94..105 [12])     <-
+      # +---> (112..125, 133..146 [14])
       def fuse
         self.class.new(rna, root.clone).tap { |tree| tree.extend_interior_loops! }
       end

data/lib/wrnap/version.rb

@@ -1,3 +1,3 @@
 module Wrnap
-  VERSION = "1.2.1"
+  VERSION = "1.2.2"
 end

data/wrnap.gemspec

@@ -20,11 +20,11 @@ Gem::Specification.new do |spec|
 
   spec.required_ruby_version = ">= 2.0"
 
-  spec.add_development_dependency "awesome_print", "~> 1.2.0"
+  spec.add_development_dependency "awesome_print", "~> 1.2"
   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_development_dependency "gem-release",   "~> 0.7"
+  spec.add_development_dependency "rake",          "~> 10.4"
+  
   spec.add_runtime_dependency "activesupport",    "~> 4.0"
   spec.add_runtime_dependency "bio",              "~> 1.4"
   spec.add_runtime_dependency "bio-stockholm",    "~> 0.0.1"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: wrnap
 version: !ruby/object:Gem::Version
-  version: 1.2.1
+  version: 1.2.2
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-12 00:00:00.000000000 Z
+date: 2015-01-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: awesome_print
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: '1.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: '1.2'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -45,9 +45,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.7.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -55,23 +52,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.7.3
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '10.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '10.4'
 - !ruby/object:Gem::Dependency
   name: activesupport
   requirement: !ruby/object:Gem::Requirement