tree_clusters 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 814af5b305dc911aa41bb70fc7afd7c5103ca0bc
-  data.tar.gz: cefdde1e0149b0ccd30b44ae0ae1e2c3646548c9
+  metadata.gz: f069c5801fa47b4861acb1ef2468526082c311b6
+  data.tar.gz: f865bbcc0da44a648847e9093a4d40511d8eaef1
 SHA512:
-  metadata.gz: 5a60b4ab7d3284f2ba2f81b122771868c6f33d4e5f3c2a8d7b36fab6bb234a123587bd7f6db81e7b5190e0c27c6287a58eb745403d9f5abdad5308e2549f59b4
-  data.tar.gz: 6e649c14f41a250e1150e798d9109f1b96f32445dfb33192c5b361f6ea2078b5e785319b18616cbe41c1c243e74b50aebc55b7e31c01e50faaa65be42d56c044
+  metadata.gz: d82b8821ab2205517bb111602bbcc83bbf28091d8503c56332fe78db24ca1681a72d1be21f6272360629fa4e1e48872e4447ba65cd4c5c2f5971ebc90652b1da
+  data.tar.gz: 694d9b68a945546b912ba998b817964cc98e1086d2ca2bd3933311834b26649c4ec0b66b26ac0889c76347c7167de8d0d50a6dba642c637e6353b58055b329cb

data/.gitignore

@@ -8,5 +8,14 @@
 /spec/reports/
 /tmp/
 
+test_files/pola*
+test_files/rnr*
+test_files/OUTPUT*
+test_files/ignore
+
+.DS_Store
+
+.ruby-*
+
 # rspec failure tracking
 .rspec_status

data/lib/tree_clusters/version.rb

@@ -1,3 +1,3 @@
 module TreeClusters
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end

data/lib/tree_clusters.rb

@@ -29,10 +29,14 @@ module TreeClusters
   #
   # @param tree [NewickTree] a NewickTree object
   #
-  # @return [Array<Clade>] array of Clade objects
+  # @yieldparam clade [Clade] a clade of the tree
+  #
+  # @return [Enumerator<Clade>] enumerator of Clade objects
   def all_clades tree
-    tree.clade_nodes.reverse.map do |node|
-      Clade.new node, tree
+    return enum_for(:all_clades, tree) unless block_given?
+
+    tree.clade_nodes.reverse.each do |node|
+      yield Clade.new node, tree
     end
   end
 
@@ -72,6 +76,14 @@ module TreeClusters
 
       TreeClusters::AttrArray.new ary
     end
+
+    def add leaf, attr, val
+      if self.has_key? leaf
+        self[leaf][attr] = val
+      else
+        self[leaf] = { attr => val }
+      end
+    end
   end
 
   # Provides convenience methods for working with Arrays of Sets
@@ -97,8 +109,10 @@ module TreeClusters
                   :all_leaves,
                   :left_leaves,
                   :right_leaves,
-                  :sibling_leaves,
+                  :all_sibling_leaves,
+                  :each_sibling_leaf_set,
                   :parent_leaves,
+                  :non_parent_leaves,
                   :other_leaves
 
     # @param node [NewickNode] a NewickNode from a NewickTree
@@ -107,19 +121,22 @@ module TreeClusters
       @name = node.name
       @all_leaves = descendant_leaves node
 
-      children = node.children
-      assert children.count == 2,
-             "Not a bifurcating tree (See: #{node.name})"
-      lchild, rchild = node.children
+      if (children = node.children).count == 2
+        lchild, rchild = node.children
 
-      @left_leaves = descendant_leaves lchild
+        @left_leaves = descendant_leaves lchild
 
-      @right_leaves = descendant_leaves rchild
+        @right_leaves = descendant_leaves rchild
+      end
 
       siblings = node.siblings
-      assert siblings.count == 1,
-             "Node #{node.name} has more than one sibling."
-      @sibling_leaves = descendant_leaves siblings.first
+      # assert siblings.count == 1,
+      #        "Node #{node.name} has more than one sibling."
+
+      @each_sibling_leaf_set = siblings.
+                               map { |node| descendant_leaves node }
+
+      @all_sibling_leaves = @each_sibling_leaf_set.flatten.uniq
 
       parent = node.parent
       assert parent,
@@ -128,6 +145,9 @@ module TreeClusters
 
       @other_leaves =
         Object::Set.new(tree.taxa) - Object::Set.new(all_leaves)
+
+      @non_parent_leaves =
+        Object::Set.new(tree.taxa) - Object::Set.new(parent_leaves)
     end
 
     # Compares two Clades field by field.
@@ -140,7 +160,8 @@ module TreeClusters
         self.all_leaves == clade.all_leaves &&
         self.left_leaves == clade.left_leaves &&
         self.right_leaves == clade.right_leaves &&
-        self.sibling_leaves == clade.sibling_leaves &&
+        self.all_sibling_leaves == clade.all_sibling_leaves &&
+        self.each_sibling_leaf_set == clade.each_sibling_leaf_set &&
         self.parent_leaves == clade.parent_leaves &&
         self.other_leaves == clade.other_leaves
       )

data/test_files/non_bifurcating.aln

@@ -0,0 +1,20 @@
+>g1
+AT-C
+>g2
+ATAC
+>g3
+ATGC
+
+>g4
+CTGC
+>g5
+CT-C
+>g6
+CTTC
+
+>g7
+TA-C
+>g8
+TA-C
+>g9
+TA-C

data/test_files/non_bifurcating.tre

@@ -0,0 +1 @@
+((g1,g2,g3)cluster3,(g4,g5,g6)cluster2,(g7,g8,g9)cluster1)cluster4;

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: tree_clusters
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-10-29 00:00:00.000000000 Z
+date: 2017-11-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -133,7 +133,8 @@ files:
 - bin/setup
 - lib/tree_clusters.rb
 - lib/tree_clusters/version.rb
-- test_files/test.rb
+- test_files/non_bifurcating.aln
+- test_files/non_bifurcating.tre
 - test_files/test.tre
 - tree_clusters.gemspec
 homepage: https://github.com/mooreryan/tree_clusters

data/test_files/test.rb

@@ -1,15 +0,0 @@
-# Require the library
-require "tree_clusters"
-
-# Make the TreeClusters methods available under the namespace
-# TreeClusters
-TreeClusters.extend TreeClusters
-
-# Read in the Newick formatted tree
-tree = NewickTree.fromFile ARGV.first
-
-# Iterate through all the clades
-TreeClusters.all_clades(tree).each do |clade|
-  # Print out the clade name and the names of all leaves in that clade
-  printf "%s\t%s\n", clade.name, clade.all_leaves.join(", ")
-end