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.


82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
# 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

Instance Attribute Details

#write_branch_length_as_subelementObject

Returns the value of attribute write_branch_length_as_subelement


74
75
76
# File 'lib/bio/db/phyloxml/phyloxml_writer.rb', line 74

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.


165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
# 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

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)

108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
# 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) ⇒ 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)

152
153
154
155
156
157
# 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