class Bio::PhyloXML::Writer

Description

Bio::PhyloXML::Writer is for writing phyloXML (version 1.10) format files.

Requirements

Libxml2 XML parser is required. Install libxml-ruby bindings from 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

www.phyloxml.org/documentation/version_100/phyloxml.xsd.html

Constants

SCHEMA_LOCATION

Attributes

write_branch_length_as_subelement[RW]

Public Class Methods

generate_xml(root, elem, subelement_array) click to toggle source

Used by to_xml methods of PhyloXML element classes. Generally not to be invoked directly.

# File lib/bio/db/phyloxml/phyloxml_writer.rb, line 165
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
new(filename, indent=true) click to toggle source

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.

# File lib/bio/db/phyloxml/phyloxml_writer.rb, line 82
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

Public Instance Methods

write(tree) click to toggle source

Write a tree to a file in phyloxml format.

require 'Bio'
writer = Bio::PhyloXML::Writer.new
writer.write(tree)
# File lib/bio/db/phyloxml/phyloxml_writer.rb, line 108
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
write_other(other_arr) click to toggle source

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)
# File lib/bio/db/phyloxml/phyloxml_writer.rb, line 152
def write_other(other_arr)
  other_arr.each do |other_obj|
    @root << other_obj.to_xml
  end
  @doc.save(@filename, :indent => @indent)
end