Class: Bio::PhyloXML::Writer

Inherits:
Object
  • Object
show all
Includes:
LibXML
Defined in:
lib/bio/db/phyloxml/phyloxml_writer.rb

Overview

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

Constant Summary collapse

SCHEMA_LOCATION =
'http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename, indent = true) ⇒ Writer

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.


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# File 'lib/bio/db/phyloxml/phyloxml_writer.rb', line 83

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

Instance Attribute Details

#write_branch_length_as_subelementObject

Returns the value of attribute write_branch_length_as_subelement


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# File 'lib/bio/db/phyloxml/phyloxml_writer.rb', line 75

def write_branch_length_as_subelement
  @write_branch_length_as_subelement
end

Class Method Details

.generate_xml(root, elem, subelement_array) ⇒ Object

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


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# File 'lib/bio/db/phyloxml/phyloxml_writer.rb', line 166

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

Instance Method Details

#write(tree) ⇒ Object

Write a tree to a file in phyloxml format.

require 'Bio'
writer = Bio::PhyloXML::Writer.new
writer.write(tree)

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# File 'lib/bio/db/phyloxml/phyloxml_writer.rb', line 109

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) ⇒ Object

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)

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# File 'lib/bio/db/phyloxml/phyloxml_writer.rb', line 153

def write_other(other_arr)
  other_arr.each do |other_obj|
    @root << other_obj.to_xml
  end
  @doc.save(@filename, :indent => @indent)
end