bioruby-phyloxml 1.0.0

data/lib/bio-phyloxml/phyloxml_writer.rb

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+#
+# = bio/db/phyloxml_writer.rb - PhyloXML writer
+#
+# Copyright::   Copyright (C) 2009
+#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
+# License::     The Ruby License
+#
+#
+# == Description
+#
+# This file containts writer for PhyloXML.
+#
+# == Requirements
+#
+# Libxml2 XML parser is required. Install libxml-ruby bindings from
+# http://libxml.rubyforge.org or
+#
+#   gem install -r libxml-ruby
+#
+# == References
+#
+# * http://www.phyloxml.org
+#
+# * https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
+
+require 'libxml'
+require 'bio-phyloxml/phyloxml_elements'
+
+module Bio
+
+  module PhyloXML
+
+  # == Description
+  #
+  # Bio::PhyloXML::Writer is for writing phyloXML (version 1.10) format files.
+  #
+  # == Requirements
+  #
+  # Libxml2 XML parser is required. Install libxml-ruby bindings from
+  # http://libxml.rubyforge.org or
+  #
+  #   gem install -r libxml-ruby
+  #
+  # == Usage
+  #
+  #   require 'bio'
+  #
+  #  # Create new phyloxml parser
+  #  phyloxml = Bio::PhyloXML::Parser.open('example.xml')
+  #
+  #  # Read in some trees from file
+  #  tree1 = phyloxml.next_tree
+  #  tree2 = phyloxml.next_tree
+  #
+  #  # Create new phyloxml writer
+  #  writer = Bio::PhyloXML::Writer.new('tree.xml')
+  #
+  #  # Write tree to the file tree.xml
+  #  writer.write(tree1)
+  #
+  #  # Add another tree to the file
+  #  writer.write(tree2)
+  #
+  # == References
+  #
+  # http://www.phyloxml.org/documentation/version_100/phyloxml.xsd.html
+
+    class Writer
+
+      include LibXML
+
+      SCHEMA_LOCATION = 'http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd'
+            
+      attr_accessor :write_branch_length_as_subelement
+
+      #
+      # Create new Writer object. As parameters provide filename of xml file
+      # you wish to create. Optional parameter is whether to indent or no.
+      # Default is true. By default branch_length is written as subelement of
+      # clade element.
+      #
+      def initialize(filename, indent=true)
+      @write_branch_length_as_subelement = true #default value
+      @filename = filename
+      @indent = indent
+
+      @doc = XML::Document.new()
+      @doc.root = XML::Node.new('phyloxml')
+      @root = @doc.root
+      @root['xmlns:xsi'] = 'http://www.w3.org/2001/XMLSchema-instance'
+      @root['xsi:schemaLocation'] = SCHEMA_LOCATION
+      @root['xmlns'] = 'http://www.phyloxml.org'
+
+      #@todo save encoding to be UTF-8. (However it is the default one).
+      #it gives error NameError: uninitialized constant LibXML::XML::Encoding
+      #@doc.encoding = XML::Encoding::UTF_8
+
+      @doc.save(@filename, :indent => true)
+      end
+
+      #
+      # Write a tree to a file in phyloxml format.
+      #
+      #  require 'Bio'
+      #  writer = Bio::PhyloXML::Writer.new
+      #  writer.write(tree)
+      #
+      def write(tree)
+        @root << phylogeny = XML::Node.new('phylogeny')        
+        
+        PhyloXML::Writer.generate_xml(phylogeny, tree, [
+            [:attr, 'rooted'],
+            [:simple, 'name', tree.name],
+            [:complex, 'id', tree.phylogeny_id],
+            [:simple, 'description', tree.description],
+            [:simple, 'date', tree.date],
+            [:objarr, 'confidence', 'confidences']])
+
+        root_clade = tree.root.to_xml(nil, @write_branch_length_as_subelement)
+        
+        phylogeny << root_clade 
+
+        tree.children(tree.root).each do |node|
+          root_clade << node_to_xml(tree, node, tree.root)
+        end
+
+        Bio::PhyloXML::Writer::generate_xml(phylogeny, tree, [
+            [:objarr, 'clade_relation', 'clade_relations'],
+            [:objarr, 'sequence_relation', 'sequence_relations'],
+            [:objarr, 'property', 'properties']] )
+
+        @doc.save(@filename, :indent => @indent)
+      end #writer#write
+
+
+      #
+      # PhyloXML Schema allows to save data in different xml format after all
+      # phylogeny elements. This method is to write these additional data.
+      #
+      #  parser = PhyloXML::Parser.open('phyloxml_examples.xml')
+      #  writer = PhyloXML::Writer.new('new.xml')
+      #
+      #  parser.each do |tree|
+      #    writer.write(tree)
+      #  end
+      #
+      #  # When all the trees are read in by the parser, whats left is saved at
+      #  # PhyloXML::Parser#other
+      #  writer.write(parser.other)
+      #
+
+      def write_other(other_arr)
+        other_arr.each do |other_obj|
+          @root << other_obj.to_xml
+        end
+        @doc.save(@filename, :indent => @indent)
+      end
+
+      #class method
+
+      #
+      # Used by to_xml methods of PhyloXML element classes. Generally not to be
+      # invoked directly. 
+      #
+      def self.generate_xml(root, elem, subelement_array)
+       #example usage: generate_xml(node, self, [[ :complex,'accession', ], [:simple, 'name',  @name], [:simple, 'location', @location]])
+      subelement_array.each do |subelem|
+        if subelem[0] == :simple         
+          root << XML::Node.new(subelem[1], subelem[2].to_s) if subelem[2] != nil and not subelem[2].to_s.empty?
+
+        elsif subelem[0] == :complex
+          root << subelem[2].send("to_xml") if subelem[2] != nil
+
+        elsif subelem[0] == :pattern
+          #seq, self, [[:pattern, 'symbol', @symbol, "\S{1,10}"]
+          if subelem[2] != nil
+            if subelem[2] =~ subelem[3]
+              root << XML::Node.new(subelem[1], subelem[2])
+            else
+              raise "#{subelem[2]} is not a valid value of #{subelem[1]}. It should follow pattern #{subelem[3]}"
+            end
+          end
+
+        elsif subelem[0] == :objarr
+          #[:objarr, 'annotation', 'annotations']])
+          obj_arr = elem.send(subelem[2])
+          obj_arr.each do |arr_elem|
+            root << arr_elem.to_xml
+          end
+
+        elsif subelem[0] == :simplearr
+          #  [:simplearr, 'common_name', @common_names]
+          subelem[2].each do |elem_val|
+            root << XML::Node.new(subelem[1], elem_val)
+          end
+        elsif subelem[0] == :attr
+          #[:attr, 'rooted']
+          obj = elem.send(subelem[1])
+          if obj != nil
+            root[subelem[1]] = obj.to_s
+          end
+        else
+          raise "Not supported type of element by method generate_xml."
+        end
+      end
+      return root
+      end
+
+      private
+
+      def node_to_xml(tree, node, parent)
+        edge = tree.get_edge(parent, node)
+        branch_length = edge.distance
+
+        clade = node.to_xml(branch_length, @write_branch_length_as_subelement)
+
+        tree.children(node).each do |new_node|
+          clade << node_to_xml(tree, new_node, node)
+        end
+
+        return clade
+      end
+
+    end
+
+  end
+end

data/lib/bio-phyloxml/version.rb

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+
+module Bio
+  module PhyloXML
+    # version number of the bio-phyloxml gem package
+    VERSION = "1.0.0"
+  end
+end

data/lib/bio/db/phyloxml/phyloxml_elements.rb

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+# for migration from old bioruby to bio-phyloxml
+if require 'bio-phyloxml/compat/stub_phyloxml_elements' then
+  require 'bio-phyloxml'
+end

data/lib/bio/db/phyloxml/phyloxml_parser.rb

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+# for migration from old bioruby to bio-phyloxml
+if require 'bio-phyloxml/compat/stub_phyloxml_parser' then
+  require 'bio-phyloxml'
+end

data/lib/bio/db/phyloxml/phyloxml_writer.rb

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+# for migration from old bioruby to bio-phyloxml
+if require 'bio-phyloxml/compat/stub_phyloxml_writer' then
+  require 'bio-phyloxml'
+end

data/lib/bioruby-phyloxml.rb

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+#
+
+if RUBY_VERSION >=  "1.9" then
+  require_relative "bio-phyloxml.rb"
+else
+  dir = File.dirname(__FILE__)
+  target = File.join(dir, "bio-phyloxml.rb")
+  require target
+end
+

data/sample/test_phyloxml_big.rb

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+#
+# = sample/test_phyloxml_big.rb - Tests for Bio::PhyloXML. Testing very big files.
+#
+# Copyright::   Copyright (C) 2009
+#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
+#               Naohisa Goto <ng@bioruby.org>
+# License::     The Ruby License
+#
+
+# libraries needed for the tests
+require 'libxml'
+require 'pathname'
+require 'test/unit'
+require 'digest/sha1'
+
+require 'bio/command'
+require 'bio/db/phyloxml/phyloxml_parser'
+require 'bio/db/phyloxml/phyloxml_writer'
+
+PhyloXMLBigDataPath = ARGV.shift
+
+if !PhyloXMLBigDataPath then
+  exit_code = 0
+elsif !File.directory?(PhyloXMLBigDataPath) then
+  exit_code = 1
+else
+  exit_code = false
+end
+
+if exit_code then
+  puts "Usage: #{$0} path_to_data (test options...)"
+  puts ""
+  puts "Requirements:"
+  puts " - Write permission to the path_to_data"
+  puts " - Internet connection for downloading test data"
+  puts " - unzip command to extract downloaded test data"
+  puts ""
+  puts "You may want to run Ruby with -rubygems and -I<path_to_bioruby_lib>."
+  puts ""
+  puts "Example of usage using /tmp:"
+  puts "    $ mkdir /tmp/phyloxml"
+  puts "    $ ruby -rubygems -I lib #{$0} /tmp/phyloxml -v"
+  puts ""
+  exit(exit_code)
+end
+
+module TestPhyloXMLBigData
+
+  module_function
+
+  def metazoa_xml
+    #puts "Metazoa 30MB"
+    filename = 'ncbi_taxonomy_metazoa.xml'
+    uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_metazoa.xml.zip"
+    download_and_unzip_if_not_found(filename, uri, "1M", "33M")
+  end
+
+  def metazoa_test_xml
+    #puts "writing Metazoa 30MB"
+    File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_metazoa.xml'
+  end
+
+  def metazoa_roundtrip_xml
+    #puts "writing Metazoa 30MB roundtrip"
+    File.join PhyloXMLBigDataPath, 'roundtrip_test_ncbi_taxonomy_metazoa.xml'
+  end
+
+  def mollusca_xml
+    #puts "Mollusca 1.5MB"
+    filename = 'ncbi_taxonomy_mollusca.xml'
+    uri = "http://www.phylosoft.org/archaeopteryx/examples/data/ncbi_taxonomy_mollusca.xml.zip"
+    download_and_unzip_if_not_found(filename, uri, "67K", "1.5M")
+  end
+
+  def mollusca_test_xml
+    #puts "Writing Mollusca 1.5MB"
+    File.join PhyloXMLBigDataPath, 'writer_test_ncbi_taxonomy_mollusca.xml'
+  end
+
+  def mollusca_roundtrip_xml
+    #puts "Writing Mollusca 1.5MB roundtrip"
+    File.join PhyloXMLBigDataPath, 'roundtrip_test_ncbi_taxonomy_mollusca.xml'
+  end
+
+  def life_xml
+    #Right now this file is not compatible with xsd 1.10
+    filename = 'tol_life_on_earth_1.xml'
+    uri = "http://www.phylosoft.org/archaeopteryx/examples/data/tol_life_on_earth_1.xml.zip"
+
+    download_and_unzip_if_not_found(filename, uri, '10M', '45M')
+  end
+
+  def life_test_xml
+    File.join PhyloXMLBigDataPath, 'writer_test_tol_life_on_earth_1.xml'
+  end
+
+  def life_roundtrip_xml
+    File.join PhyloXMLBigDataPath, 'roundtrip_test_tol_life_on_earth_1.xml'
+  end
+
+  def unzip_file(file, target_dir)
+    flag = system('unzip', "#{file}.zip", "-d", target_dir)
+    unless flag then
+      raise "Failed to unzip #{file}.zip"
+    end
+    file
+  end
+
+  def download_and_unzip_if_not_found(basename, uri, zipsize, origsize)
+    file = File.join PhyloXMLBigDataPath, basename
+    return file if File.exists?(file)
+
+    if File.exists?("#{file}.zip")
+      unzip_file(file, PhyloXMLBigDataPath)
+      return file
+    end
+
+    puts "File #{basename} does not exist. Do you want to download it? (If yes, ~#{zipsize}B zip file will be downloaded and extracted (to #{origsize}B), if no, the test will be skipped.) y/n?"
+    res = gets
+    if res.to_s.chomp.downcase == "y"
+      File.open("#{file}.zip", "wb") do |f|
+        f.write(Bio::Command.read_uri(uri))
+      end
+      puts "File downloaded."
+      self.unzip_file(file, PhyloXMLBigDataPath)
+      return file
+    else
+      return nil
+      #return File.join PHYLOXML_TEST_DATA, "#{basename}.stub"
+    end
+  end
+
+end #end module TestPhyloXMLBigData
+
+module Bio
+
+  class TestPhyloXMLBig < Test::Unit::TestCase
+
+    def do_test_next_tree(readfilename)
+      raise "the test is skipped" unless readfilename
+      filesizeMB = File.size(readfilename) / 1048576.0
+      printf "Reading %s (%2.1f MB)\n", readfilename, filesizeMB
+             
+      begin
+        phyloxml = Bio::PhyloXML::Parser.open(readfilename)
+      rescue NoMethodError
+        phyloxml = Bio::PhyloXML::Parser.new(readfilename)
+      end
+      tree = nil
+      assert_nothing_raised {
+        tree = phyloxml.next_tree
+      }
+      tree
+    end
+    private :do_test_next_tree
+
+    def do_test_write(tree, writefilename)
+      printf "Writing to %s\n", writefilename
+      writer = Bio::PhyloXML::Writer.new(writefilename)
+      assert_nothing_raised {
+        writer.write(tree)
+      }
+
+      # checks file size and sha1sum
+      str = File.open(writefilename, 'rb') { |f| f.read }
+      sha1 = Digest::SHA1.hexdigest(str)
+      puts "Wrote #{str.length} bytes."
+      puts "sha1: #{sha1}"
+    end
+    private :do_test_write
+
+    def test_mollusca
+      tree = do_test_next_tree(TestPhyloXMLBigData.mollusca_xml)
+      do_test_write(tree, TestPhyloXMLBigData.mollusca_test_xml)
+
+      tree2 = do_test_next_tree(TestPhyloXMLBigData.mollusca_test_xml)
+      do_test_write(tree2, TestPhyloXMLBigData.mollusca_roundtrip_xml)
+    end
+
+    def test_metazoa
+      tree = do_test_next_tree(TestPhyloXMLBigData.metazoa_xml)
+      do_test_write(tree, TestPhyloXMLBigData.metazoa_test_xml)
+
+      tree2 = do_test_next_tree(TestPhyloXMLBigData.metazoa_test_xml)
+      do_test_write(tree2, TestPhyloXMLBigData.metazoa_roundtrip_xml)
+    end
+
+    if false
+      # Disabled because of the error.
+      # LibXML::XML::Error: Fatal error: Input is not proper UTF-8,
+      # indicate encoding !
+      # Bytes: 0xE9 0x6B 0x65 0x73 at tol_life_on_earth_1.xml:132170.
+      #
+      def test_life
+        tree = do_test_next_tree(TestPhyloXMLBigData.life_xml)
+        do_test_write(tree, TestPhyloXMLBigData.life_test_xml)
+        
+        tree2 = do_test_next_tree(TestPhyloXMLBigData.life_test_xml)
+        do_test_write(tree2, TestPhyloXMLBigData.life_roundtrip_xml)
+      end
+    end #if false
+
+  end
+
+end