iroki 0.0.6 → 0.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: b109a3a6bacea94e8aaa32c9d316a1fafb1bb899
+  metadata.gz: e95553e4a9cc4572479c11aa9f5701e897e7fbd9
+  data.tar.gz: ff5b30ae95cdfb53e2c443877100f55cf3846e67
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+  data.tar.gz: 363ef46a8ff54ab9858c46d0f6cfdc04f270cb03933ed2378af3a818a9ba3d6ec70a2f1b4d050ebd1da4076f2862eb8a56e2e7e55773bdbccfe1809063c48beb

data/.gitignore

@@ -10,3 +10,5 @@
 *.lock
 .ruby-gemset
 newicks
+test_files
+sandbox

data/README.md

@@ -100,3 +100,7 @@ Add `newick_to_phyloxml` script.
 ### 0.0.6 ###
 
 Add branch length and bootstraps to `newick_to_phyloxml`.
+
+### 0.0.7 ###
+
+Add `reorder_nodes` script.

data/exe/newick_to_phyloxml_color

@@ -0,0 +1,132 @@
+#!/usr/bin/env ruby
+
+# NOTE make sure the newick has no spaces for jsPhyloXML
+
+# NOTE for Archaeopteryx, you need <name>#{boot}</name> to show
+# bootsraps, but for jsPhyloXML, just the confidence is needed
+
+require "set"
+require "bio"
+require "color"
+require "abort_if"
+
+include AbortIf
+
+logger.warn { "This is an internal Iroki script. It is not meant for " +
+              "general use." }
+
+def leaf? tree, node
+  tree.children(node).empty?
+end
+
+fname = ARGV.first
+
+tree_str = File.open(fname, 'rt').read
+
+newick = Bio::Newick.new(tree_str, parser: :naive)
+
+$tree = newick.tree
+
+$xml_start = %q{<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
+<phylogeny rooted="false">
+<clade>
+}
+
+$xml_end = %q{</clade>
+</phylogeny>
+</phyloxml>
+}
+
+def leaf? tree, node
+  tree.descendents(node).count.zero?
+end
+
+def name_and_color node
+  m = node.name.match(/(.*)___ryan_([a-fA-F0-9]+)/)
+  if m
+    name = m[1]
+    hex  = m[2]
+
+    col = Color::RGB.by_hex hex
+
+    [name, col]
+  else
+    nil
+  end
+end
+
+def make_xml_string descendents, start_node
+  while (node = descendents.shift)
+    unless $already_added.include? node
+      ary = name_and_color(node)
+      new_name, col = ary
+
+      if leaf? $tree, node
+        # TODO this will raise something if no dist, rescue it
+        dist = $tree.distance(start_node, node)
+        dist = 1
+
+        if ary # then it needs color
+          color_xml = %Q{<color>
+<red>#{col.red}</red>
+<green>#{col.green}</green>
+<blue>#{col.blue}</blue>
+</color>
+<property ref="style:font_color" datatype="xsd:token" applies_to="node">##{col.hex}</property>}
+        else
+          color_xml = ""
+        end
+
+        $xml_start << "<clade>
+<name>#{ary ? new_name : node.name}</name>
+<branch_length>#{dist}</branch_length>
+#{color_xml}
+</clade>\n"
+        $already_added << node
+        $prev_node = node
+      else
+        boot = node.bootstrap
+        if boot
+          boot_xml = %Q{\n<confidence type="bootstrap">#{boot}</confidence>}
+        else
+          boot_xml = ""
+        end
+
+        # TODO this will raise something if no dist, rescue it
+        dist = $tree.distance(start_node, node)
+        dist = 1
+
+        if ary # then it needs color
+          color_xml = "<color>
+<red>#{col.red}</red>
+<green>#{col.green}</green>
+<blue>#{col.blue}</blue>
+</color>"
+        else
+          color_xml = ""
+        end
+
+        $xml_start << "<clade>
+<branch_length>#{dist}</branch_length>
+#{boot_xml}
+#{color_xml}"
+
+        STDERR.puts "LOG -- recurse"
+        make_xml_string $tree.descendents(node), node
+        $xml_start << "</clade>\n"
+        $already_added << node
+      end
+    end
+  end
+end
+
+$already_added = Set.new
+
+start_node = $tree.root
+
+$descendents = $tree.descendents(start_node)
+
+make_xml_string $descendents, start_node
+
+puts $xml_start
+puts "#{$xml_end}"

data/exe/reorder_nodes

@@ -0,0 +1,206 @@
+#!/usr/bin/env ruby
+
+require "bio"
+require "trollop"
+require "abort_if"
+
+include AbortIf
+
+module Math
+  def self.max ary
+    ary.max
+  end
+
+  def self.median ary
+    len = ary.length
+    if len > 0
+      sorted = ary.sort
+
+      if len.odd?
+        sorted[len / 2]
+      else
+        (sorted[(len-1) / 2] + sorted[len/2]) / 2.0
+      end
+    end
+  end
+
+  def self.mean ary
+    len = ary.length
+    if len > 0
+      ary.reduce(:+) / len.to_f
+    end
+  end
+
+  def self.dist_for_comp metric, ary
+    self.send(metric, ary)
+  end
+
+end
+
+class Bio::Tree
+  def root_to_node_dist node
+    self.distance(self.root, node)
+  end
+
+  def root_to_node_dists nodes
+    nodes.map do |node|
+      root_to_node_dist node
+    end
+  end
+
+  def __to_newick(parents, source, depth, format_leaf,
+                  options, &block)
+    result = []
+    if indent_string = __get_option(:indent, options) then
+      indent0 = indent_string * depth
+      indent  = indent_string * (depth + 1)
+      newline = "\n"
+    else
+      indent0 = indent = newline = ''
+    end
+    out_edges = self.out_edges(source)
+    if block_given? then
+      out_edges.sort! { |edge1, edge2| yield(edge1[1], edge2[1]) }
+    else
+      # this sorts within clades
+      out_edges.sort! do |edge1, edge2|
+        n1 = edge1[1]
+        n2 = edge2[1]
+        # o1 = edge1[1].order_number
+        # o2 = edge2[1].order_number
+        d1 = edge1[2].distance
+        d2 = edge2[2].distance
+        # STDERR.puts
+        # STDERR.puts [:hi, edge1[0], edge1[1], d1, edge2[0], edge2[1], d2].inspect
+
+        n1_leaves = self.leaves(n1)
+        n2_leaves = self.leaves(n2)
+
+        dists_1 = root_to_node_dists n1_leaves
+        dists_2 = root_to_node_dists n2_leaves
+
+        the_dist_1 = Math.dist_for_comp COMP_METHOD, dists_1
+        the_dist_2 = Math.dist_for_comp COMP_METHOD, dists_2
+
+        # TODO check if leaves is empty
+        if the_dist_1 && the_dist_2
+          # STDERR.puts [:bye, the_dist_1, the_dist_2]
+          if LONG_ON_TOP
+            the_dist_2 <=> the_dist_1
+          else
+            the_dist_1 <=> the_dist_2
+          end
+        elsif the_dist_1 # first has leaves, it is "longer"
+          if LONG_ON_TOP
+            -1
+          else
+            1
+          end
+        elsif the_dist_2 # second has leaves, second is longer
+          if LONG_ON_TOP
+            1
+          else
+            -1
+          end
+        else # neither has leaves, use dist
+          if d1 and d2 then # check that both dists exist
+            if LONG_ON_TOP
+              d2 <=> d1
+            else
+              d1 <=> d2
+            end
+          else # just use the names
+            edge1[1].name.to_s <=> edge2[1].name.to_s
+          end
+        end
+      end
+    end
+    out_edges.each do |src, tgt, edge|
+      if parents.include?(tgt) then
+        ;;
+      elsif self.out_degree(tgt) == 1 then # target is a leaf?
+        # STDERR.puts "what is this? |#{src}| |#{tgt}|"
+        result << indent + __send__(format_leaf, tgt, edge, options)
+      else # target is an interior node
+        # STDERR.puts "recurse |#{src}| |#{tgt}|"
+        result <<
+          __to_newick([ src ].concat(parents), tgt, depth + 1,
+                      format_leaf, options) +
+          __send__(format_leaf, tgt, edge, options)
+      end
+    end
+    indent0 + "(" + newline + result.join(',' + newline) +
+      (result.size > 0 ? newline : '') + indent0 + ')'
+  end
+  private :__to_newick
+end
+
+opts = Trollop.options do
+  banner <<-EOS
+
+  Synopsis
+    reorder_nodes [-o order] [-c comparison_method] -i newick.tre > newick.ordered.tre
+
+  Info
+    Given a newick file, reorder the nodes as directed.
+
+  Option details
+    --infile     A newick file with a single tree
+    --order      Order in which to display nodes: increasing or decreasing
+    --comparison Method to sort inner nodes: mean, median, max
+
+  Options
+
+  EOS
+
+  opt(:infile,
+      "input file",
+      type: :string)
+
+  opt(:order,
+      "increasing or decreasing",
+      type: :string,
+      default: "increasing")
+
+  opt(:comparison,
+      "mean, median, or max",
+      type: :string,
+      default: "max")
+end
+
+abort_unless %w[increasing decreasing].include?(opts[:order]),
+             "--order must be one of increasing or decreasing, " +
+             "got #{opts[:order]}.\nTry reorder_nodes --help for help."
+
+if opts[:order] == "increasing"
+  LONG_ON_TOP = true
+else
+  LONG_ON_TOP = false
+end
+
+abort_unless %w[mean median max].include?(opts[:comparison]),
+             "--comparison must be one of mean, median, or max, " +
+             "got #{opts[:comparison]}.\n" +
+             "Try reorder_nodes --help for help."
+
+COMP_METHOD = opts[:comparison]
+
+abort_unless opts[:infile],
+             "--infile is a required option. " +
+             "Try reorder_nodes --help for help."
+
+abort_unless File.exists?(opts[:infile]),
+             "--infile #{opts[:infile]} does not exist.\n" +
+             "Try reorder_nodes --help for help."
+
+fname = opts[:infile]
+
+tree_str = File.open(fname, 'rt').read
+
+# this only will work if there is only one tree
+newick = Bio::Newick.new(tree_str, parser: :naive, indent: false)
+
+tree = newick.tree
+
+# warn tree_str
+puts tree.newick

data/iroki.gemspec

@@ -30,5 +30,6 @@ Gem::Specification.new do |spec|
 
   spec.add_runtime_dependency "abort_if", "~> 0.1.0"
   spec.add_runtime_dependency "bio", "~> 1.5"
+  spec.add_runtime_dependency "color", "~> 1.8"
   spec.add_runtime_dependency "trollop", "~> 2.1", ">= 2.1.2"
 end

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.6"
+  VERSION = "0.0.7"
   COPYRIGHT = "2015 - 2016 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-05-22 00:00:00.000000000 Z
+date: 2016-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -128,6 +128,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: color
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
@@ -155,6 +169,8 @@ email:
 executables:
 - iroki
 - newick_to_phyloxml
+- newick_to_phyloxml_color
+- reorder_nodes
 extensions: []
 extra_rdoc_files: []
 files:
@@ -174,6 +190,8 @@ files:
 - bin/setup
 - exe/iroki
 - exe/newick_to_phyloxml
+- exe/newick_to_phyloxml_color
+- exe/reorder_nodes
 - iroki.gemspec
 - lib/iroki.rb
 - lib/iroki/color/color.rb