bio-nwk 0.1.0 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: fdc68bf449c666e6bd715b75be20f5cd8470ee96b8ccd70e0c33b4ef0f5a371a
+  metadata.gz: 8d9592e998026208adab8760c3c98f61c7dca740ede2e2634146252abeea18cc
+  data.tar.gz: be558a160cdc49fed06d255f84f72bde9a062c2ca7a8422db865292c86a2a9aa
 SHA512:
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-  data.tar.gz: d27ccdc661874bdb6965419b885463df1f7e90f306626a021789ad9f343727b4ed5d0b955f3473977427b422eacdf29d96bbdac12d4b8ecaaebebf90d6f4a070
+  metadata.gz: 92351aaa11e1743679f87aebaa0919dee8c903378b819e1ea857fea1f4066c1276485ab0328dc50e63fcdee0dd3ba3bb7fd3160aab4a6b184318ddc0f4d1a219
+  data.tar.gz: a48f163a2a2498c50971f45f922fe6062bdc698dd06a2a762daed8311a8528c3133800d5a3f3b290da1e22f0454cb59ac66f895a52526cd815230b610b7be96a

data/lib/bio/nwk/version.rb

@@ -1,5 +1,5 @@
 module Bio
   module Nwk
-    VERSION = "0.1.0"
+    VERSION = "0.1.3"
   end
 end

data/lib/bio/nwk.rb

@@ -17,6 +17,10 @@ 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!(' ', '_')
@@ -39,6 +43,15 @@ 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([])
@@ -120,6 +133,34 @@ class Bio::Tree
     end
   end
 
+  def getAlldistances()
+    distances = Array.new
+    each_edge do |node0, node1, edge|
+      next if node0 == root or node1 == root
+      distances << edge.distance
+    end
+    return(distances)
+  end
+
+  def normalizeBranchLength!()
+    min, max = getAlldistances().minmax
+    each_edge do |node0, node1, edge|
+      edge.distance = (edge.distance-min+1e-10).to_f/(max-min)
+    end
+  end
+
+  def normalizeBranchLengthGainAndLoss!()
+    min, max = getAlldistances().select{|i|i>=0}.minmax
+    each_edge do |node0, node1, edge|
+      edge.distance = (edge.distance-min+1e-10).to_f/(max-min) + 1 if edge.distance >= 0
+    end
+
+    min, max = getAlldistances().select{|i|i<0}.minmax
+    each_edge do |node0, node1, edge|
+      edge.distance = (edge.distance-min+1e-10).to_f/(max-min) if edge.distance < 0
+    end
+  end
+
   private
   def translate
     #  TRANSLATE
@@ -164,3 +205,10 @@ 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: 0.1.0
+  version: 0.1.3
 platform: ruby
 authors:
 - Sishuo Wang
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2020-07-06 00:00:00.000000000 Z
+date: 2022-03-14 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: []