bio-nwk 0.1.1 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 03f6be5c7eebbea8000cc8df4593339ecfc3ecd905b00ddb4ff17c2ccb5acc2d
-  data.tar.gz: eb4ed5e27f07a141d3dd9e9bac24e4f9fb979c1dd2e1070d2f43c5d10d309bef
+  metadata.gz: b5f845416e561baa214dee9ad326763f784b5ca2f891bdb01c4deb9572f9ca23
+  data.tar.gz: e7720ae89b70955493c510b4291ae8f2125e00a6d83e88d4274fa8b3490b137a
 SHA512:
-  metadata.gz: fc5f5ff47d1df75f9b0a0660345e6e8b839fd0bc5cce43201a6865681c3a0d805947a73eb6a58aab1e302194785f6514c1fac493226d580297e3ed6c2b602028
-  data.tar.gz: f6b20529784c8339cdb17c4ef53c69942f1b896953e8821667e4b9921a1aba520eda97a6c79f96a3111a78b74262c92fec1fe1bd6b0e82ec60023505f94d9355
+  metadata.gz: a252ea335e65cbf252f3482a5fb93d5c33499df3cc401932de7db4c491628c1e3c72e9628613cf66bc632a9723bf2c541cd76c583c8aca3e8d1a456d17d71676
+  data.tar.gz: 960aa5a028aa7d475654d80683983f0b2f1900aaa665f09a37fa776d67bec11992ed0b9328c9d1aeb2a9fbf1bf884ee39629236f2ab70e41b6445289e3b95cdc

data/lib/bio/nwk/version.rb

@@ -1,5 +1,5 @@
 module Bio
   module Nwk
-    VERSION = "0.1.1"
+    VERSION = "0.1.4"
   end
 end

data/lib/bio/nwk.rb

@@ -7,6 +7,7 @@ class Bio::Tree
   DELIMITER = ';'
   attr_accessor :tip2index, :index2tip
 
+
   def tips(node)
     rv = Array.new
     if node.isTip?(self)
@@ -17,12 +18,19 @@ class Bio::Tree
     return(rv)
   end
 
+
+  def all_nodes_of_subtree(node)
+    [leaves(node), tips(node)].flatten
+  end
+
+
   def cleanName!
     allTips.each do |tip|
       tip.name.gsub!(' ', '_')
     end
   end
 
+
   def twoTaxaNode(node)
     if node.isTip?(self)
       return(node)
@@ -30,6 +38,7 @@ class Bio::Tree
       return children(node).map{|child|tips(child).sort_by{|i|i.name}.shift}.sort_by{|i|i.name}
     end
   end
+
   
   def twoTaxaNodeName(node)
     if node.isTip?(self)
@@ -39,6 +48,17 @@ class Bio::Tree
     end
   end
 
+
+  def twoTaxaNodeNameStr(node, sep='|')
+    a = twoTaxaNodeName(node)
+    if a.is_a?(Array)
+      return(a.join(sep))
+    else
+      return(a)
+    end
+  end
+
+
   def sisters(node)
     if node == root
       return([])
@@ -47,10 +67,12 @@ class Bio::Tree
     end
   end
 
+
   def sister(node)
     return(sisters(node)[0])
   end
 
+
   def internal_nodes
     a = Array.new
     nodes.each do |node|
@@ -61,6 +83,7 @@ class Bio::Tree
     return(a)
   end
 
+
   def allSubtreeRepresentatives
     arr = Array.new
     nodes.each do |node|
@@ -69,6 +92,7 @@ class Bio::Tree
     return(arr)
   end
 
+
   def allTips
     a = Array.new
     nodes.each do |node|
@@ -77,6 +101,7 @@ class Bio::Tree
     return(a)
   end
 
+
   def outputNexus(isTranslate=false, isTip2Index=false)
     puts "#NEXUS"
     puts
@@ -88,6 +113,7 @@ class Bio::Tree
     newickIndexToTip if isTip2Index
   end
 
+
   def cleanNewick
     output = output_newick
     output.gsub!(/[\n\s]/, '')
@@ -95,6 +121,7 @@ class Bio::Tree
     return(output)
   end
 
+
   def tipToIndex
     @tip2index = Hash.new
     @index2tip = Hash.new
@@ -104,6 +131,7 @@ class Bio::Tree
     end
   end
 
+
   def newickTipToIndex()
     tipToIndex
     allTips.each do |tip|
@@ -112,6 +140,7 @@ class Bio::Tree
     end
   end
 
+
   def newickIndexToTip()
     tipToIndex if @index2tip.empty?
     allTips.each do |tip|
@@ -120,6 +149,7 @@ class Bio::Tree
     end
   end
 
+
   def getAlldistances()
     distances = Array.new
     each_edge do |node0, node1, edge|
@@ -129,6 +159,7 @@ class Bio::Tree
     return(distances)
   end
 
+
   def normalizeBranchLength!()
     min, max = getAlldistances().minmax
     each_edge do |node0, node1, edge|
@@ -136,6 +167,7 @@ class Bio::Tree
     end
   end
 
+
   def normalizeBranchLengthGainAndLoss!()
     min, max = getAlldistances().select{|i|i>=0}.minmax
     each_edge do |node0, node1, edge|
@@ -148,6 +180,27 @@ class Bio::Tree
     end
   end
 
+
+  def getNameTipRela()
+    tip2name, name2tip = [Hash.new, Hash.new]
+    allTips.each do |tip|
+      tip2name[tip] = tip.name
+      name2tip[tip.name] = tip
+    end
+    return([name2tip, tip2name])
+  end
+
+
+  def getNameNodeRela()
+    node2name, name2node = [Hash.new, Hash.new]
+    nodes.each do |node|
+      node2name[node] = node.name
+      name2node[node.name] = node
+    end
+    return([name2node, node2name])
+  end
+
+
   private
   def translate
     #  TRANSLATE
@@ -192,3 +245,11 @@ def getTreeObjFromNwkString(nwk_str)
 end
 
 
+def getTreeObjFromMcmctree(tree_file)
+  first_line = `head -1 #{tree_file}`.chomp
+  tree_txt = `tail -1 #{tree_file}`.chomp
+  treeio = Bio::Newick.new(tree_txt).tree
+  return([first_line, treeio])
+end
+
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-nwk
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.4
 platform: ruby
 authors:
 - Sishuo Wang
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2020-07-06 00:00:00.000000000 Z
+date: 2022-04-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -87,11 +87,11 @@ files:
 - lib/bio-nwk.rb
 - lib/bio/nwk.rb
 - lib/bio/nwk/version.rb
-homepage: 
+homepage:
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -106,9 +106,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.3
-signing_key: 
+rubygems_version: 3.2.3
+signing_key:
 specification_version: 4
 summary: Some codes for parsing newick tree.
 test_files: []