iroki 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -9,3 +9,4 @@
 /tmp/
 *.lock
 .ruby-gemset
+newicks

data/README.md

@@ -39,6 +39,18 @@ Or install it yourself as:
 
     $ gem install iroki
 
+## Other programs ##
+
+### Newick format to PhyloXML ###
+
+- `exe/newick_to_phyloxml`
+
+This will be installed when you run `gem install iroki`.
+
+*Usage*: `newick_to_phyloxml tree.newick > tree.phyloxml`
+
+*Note*: No specs for this as of yet.
+
 ## Development ##
 
 After checking out the repo, run `bin/setup` to install
@@ -76,3 +88,11 @@ executable, and use RubyGems for installation.
 ### 0.0.3 ###
 
 Add a [Dockerfile](https://github.com/mooreryan/iroki/blob/master/Dockerfile) and a [wrapper script](https://github.com/mooreryan/iroki/blob/master/exe/iroki_docker) for running Iroki with Docker.
+
+### 0.0.4 ###
+
+Fix the `iroki_docker` install bug.
+
+### 0.0.5 ###
+
+Add `newick_to_phyloxml` script.

data/exe/newick_to_phyloxml

@@ -0,0 +1,57 @@
+#!/usr/bin/env ruby
+
+require "set"
+require "bio"
+
+def leaf? tree, node
+  tree.children(node).empty?
+end
+
+newick = ARGV.first
+
+treeio = Bio::FlatFile.open(Bio::Newick, newick)
+
+newick = treeio.next_entry
+$tree = newick.tree
+
+$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>
+}
+
+added_nodes = Set.new
+
+def leaf? tree, node
+  tree.descendents(node).count.zero?
+end
+
+def make_xml_string descendents
+  while (node = descendents.shift)
+    unless $already_added.include? node
+      if leaf? $tree, node
+        $xml_start << "<clade>\n<name>#{node.name}</name>\n</clade>\n"
+        $already_added << node
+      else
+        STDERR.puts "LOG -- recurse"
+        $xml_start << "<clade>\n"
+        make_xml_string $tree.descendents(node)
+        $xml_start << "</clade>\n"
+        $already_added << node
+      end
+    end
+  end
+end
+
+$already_added = Set.new
+
+$descendents = $tree.descendents($tree.root)
+
+make_xml_string $descendents
+
+puts $xml_start
+puts "#{$xml_end}"

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.4"
+  VERSION = "0.0.5"
   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: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-05-18 00:00:00.000000000 Z
+date: 2016-05-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -154,6 +154,7 @@ email:
 - moorer@udel.edu
 executables:
 - iroki
+- newick_to_phyloxml
 extensions: []
 extra_rdoc_files: []
 files:
@@ -172,6 +173,7 @@ files:
 - bin/iroki_docker
 - bin/setup
 - exe/iroki
+- exe/newick_to_phyloxml
 - iroki.gemspec
 - lib/iroki.rb
 - lib/iroki/color/color.rb