class Bio::PhyloXML::Parser

Description

Bio::PhyloXML::Parser is for parsing phyloXML 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')

# Print the names of all trees in the file
phyloxml.each do |tree|
  puts tree.name
end

References

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

Attributes

other[R]

After parsing all the trees, if there is anything else in other xml format, it is saved in this array of PhyloXML::Other objects

Public Class Methods

for_io(io, validate=true) click to toggle source

Initializes LibXML::Reader and reads from the IO until it reaches the first phylogeny element.

Create a new Bio::PhyloXML::Parser object.

p = Bio::PhyloXML::Parser.for_io($stdin)

Arguments:

  • (required) io: IO object

  • (optional) validate: For IO reader, the “validate” option is ignored and no validation is executed.

Returns

Bio::PhyloXML::Parser object

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 218
def self.for_io(io, validate=true)
  obj = new(nil, validate)
  obj.instance_eval {
    @reader = XML::Reader.io(io,
                             { :options =>
                               LibXML::XML::Parser::Options::NONET })
    _skip_leader
  }
  obj
end
new(str, validate=true) click to toggle source

Initializes LibXML::Reader and reads the PhyloXML-formatted string until it reaches the first phylogeny element.

Create a new Bio::PhyloXML::Parser object.

str = File.read("./phyloxml_examples.xml")
p = Bio::PhyloXML::Parser.new(str)

Deprecated usage: Reads data from a file. <em>str<em> is a filename.

p = Bio::PhyloXML::Parser.new("./phyloxml_examples.xml")

Taking filename is deprecated. Use ::open.


Arguments:

  • (required) str: PhyloXML-formatted string

  • (optional) validate: Whether to validate the file against schema or not. Default value is true.

Returns

Bio::PhyloXML::Parser object

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 318
def initialize(str, validate=true)

  @other = []

  return unless str

  # For compatibility, if filename-like string is given,
  # treat it as a filename.
  if /[\<\>\r\n]/ !~ str and File.exist?(str) then
    # assume that str is filename
    warn "Bio::PhyloXML::Parser.new(filename) is deprecated. Use Bio::PhyloXML::Parser.open(filename)."
    filename = _secure_filename(str)
    _validate(:file, filename) if validate
    @reader = XML::Reader.file(filename)
    _skip_leader
    return
  end

  # initialize for string
  @reader = XML::Reader.string(str,
                               { :options =>
                                 LibXML::XML::Parser::Options::NONET })
  _skip_leader
end
open(filename, validate=true) { |obj| ... } click to toggle source

Initializes LibXML::Reader and reads the file until it reaches the first phylogeny element.

Example: Create a new Bio::PhyloXML::Parser object.

p = Bio::PhyloXML::Parser.open("./phyloxml_examples.xml")

If the optional code block is given, Bio::PhyloXML object is passed to the block as an argument. When the block terminates, the Bio::PhyloXML object is automatically closed, and the open method returns the value of the block.

Example: Get the first tree in the file.

tree = Bio::PhyloXML::Parser.open("example.xml") do |px|
  px.next_tree
end

Arguments:

  • (required) filename: Path to the file to parse.

  • (optional) validate: Whether to validate the file against schema or not. Default value is true.

Returns

(without block) Bio::PhyloXML::Parser object

Returns

(with block) the value of the block

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 102
def self.open(filename, validate=true)
  obj = new(nil, validate)
  obj.instance_eval {
    filename = _secure_filename(filename)
    _validate(:file, filename) if validate
    # XML::Parser::Options::NONET for security reason
    @reader = XML::Reader.file(filename,
                               { :options =>
                                 LibXML::XML::Parser::Options::NONET })
    _skip_leader
  }
  if block_given? then
    begin
      ret = yield obj
    ensure
      obj.close if obj and !obj.closed?
    end
    ret
  else
    obj
  end
end
open_uri(uri, validate=true) { |obj| ... } click to toggle source

Initializes LibXML::Reader and reads the file until it reaches the first phylogeny element.

Create a new Bio::PhyloXML::Parser object.

p = Bio::PhyloXML::Parser.open_uri("http://www.phyloxml.org/examples/apaf.xml")

If the optional code block is given, Bio::PhyloXML object is passed to the block as an argument. When the block terminates, the Bio::PhyloXML object is automatically closed, and the ::open_uri method returns the value of the block.


Arguments:

  • (required) uri: (URI or String) URI to the data to parse

  • (optional) validate: For URI reader, the “validate” option is ignored and no validation is executed.

Returns

(without block) Bio::PhyloXML::Parser object

Returns

(with block) the value of the block

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 143
def self.open_uri(uri, validate=true)
  case uri
  when URI
    uri = uri.to_s
  else
    # raises error if not a String
    uri = uri.to_str
    # raises error if invalid URI
    URI.parse(uri)
  end

  obj = new(nil, validate)
  obj.instance_eval {
    @reader = XML::Reader.file(uri)
    _skip_leader
  }
  if block_given? then
    begin
      ret = yield obj
    ensure
      obj.close if obj and !obj.closed?
    end
  else
    obj
  end
end

Public Instance Methods

[](i) click to toggle source

Access the specified tree in the file. It parses trees until the specified tree is reached.

# Get 3rd tree in the file (starts counting from 0).
parser = PhyloXML::Parser.open('phyloxml_examples.xml')
tree = parser[2]
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 364
def [](i)
  tree = nil
  (i+1).times do
   tree =  self.next_tree
  end
  return tree
end
close() click to toggle source

Closes the LibXML::Reader inside the object. It also closes the opened file if it is created by using ::open method.

When closed object is closed again, or closed object is used, it raises LibXML::XML::Error.


Returns

nil

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 188
def close
  @reader.close
  @reader = ClosedPhyloXMLParser.new
  nil
end
closed?() click to toggle source

If the object is closed by using the close method or equivalent, returns true. Otherwise, returns false.


Returns

true or false

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 198
def closed?
  if @reader.kind_of?(ClosedPhyloXMLParser) then
    true
  else
    false
  end
end
each() { |tree| ... } click to toggle source

Iterate through all trees in the file.

phyloxml = Bio::PhyloXML::Parser.open('example.xml')
phyloxml.each do |tree|
  puts tree.name
end
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 351
def each
  while tree = next_tree
    yield tree
  end
end
next_tree() click to toggle source

Parse and return the next phylogeny tree. If there are no more phylogeny element, nil is returned. If there is something else besides phylogeny elements, it is saved in the #other.

p = Bio::PhyloXML::Parser.open("./phyloxml_examples.xml")
tree = p.next_tree

Returns

Bio::PhyloXML::Tree

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 381
def next_tree()

  if not is_element?('phylogeny')
    if @reader.node_type == XML::Reader::TYPE_END_ELEMENT
      if is_end_element?('phyloxml')
        return nil
      else
        @reader.read
        @reader.read
        if is_end_element?('phyloxml')
          return nil
        end
      end
    end        
    # phyloxml can hold only phylogeny and "other" elements. If this is not
    # phylogeny element then it is other. Also, "other" always comes after
    # all phylogenies        
    @other << parse_other        
    #return nil for tree, since this is not valid phyloxml tree.
    return nil
  end

  tree = Bio::PhyloXML::Tree.new

  # keep track of current node in clades array/stack. Current node is the
  # last element in the clades array
  clades = []
  clades.push tree
  
  #keep track of current edge to be able to parse branch_length tag
  current_edge = nil

  # we are going to parse clade iteratively by pointing (and changing) to
  # the current node in the tree. Since the property element is both in
  # clade and in the phylogeny, we need some boolean to know if we are
  # parsing the clade (there can be only max 1 clade in phylogeny) or
  # parsing phylogeny
  parsing_clade = false

  while not is_end_element?('phylogeny') do
    break if is_end_element?('phyloxml')
    
    # parse phylogeny elements, except clade
    if not parsing_clade

      if is_element?('phylogeny')
        @reader["rooted"] == "true" ? tree.rooted = true : tree.rooted = false
        @reader["rerootable"] == "true" ? tree.rerootable = true : tree.rerootable = false
        parse_attributes(tree, ["branch_length_unit", 'type'])
      end

      parse_simple_elements(tree, [ "name", 'description', "date"])

      if is_element?('confidence')
        tree.confidences << parse_confidence
      end

    end

    if @reader.node_type == XML::Reader::TYPE_ELEMENT
      case @reader.name
      when 'clade'
        #parse clade element

        parsing_clade = true

        node= Bio::PhyloXML::Node.new

        branch_length = @reader['branch_length']

        parse_attributes(node, ["id_source"])

        #add new node to the tree
        tree.add_node(node)
        # The first clade will always be root since by xsd schema phyloxml can
        # have 0 to 1 clades in it.
        if tree.root == nil
          tree.root = node
        else
          current_edge = tree.add_edge(clades[-1], node,
                                       Bio::Tree::Edge.new(branch_length))
        end
        clades.push node
        #end if clade element
      else
       parse_clade_elements(clades[-1], current_edge) if parsing_clade
      end
    end

    #end clade element, go one parent up
    if is_end_element?('clade')

       #if we have reached the closing tag of the top-most clade, then our
      # curent node should point to the root, If thats the case, we are done
      # parsing the clade element
      if clades[-1] == tree.root
        parsing_clade = false
      else
        # set current node (clades[-1) to the previous clade in the array
        clades.pop
      end
    end          

    #parsing phylogeny elements
    if not parsing_clade

      if @reader.node_type == XML::Reader::TYPE_ELEMENT
        case @reader.name
        when 'property'
          tree.properties << parse_property

        when 'clade_relation'
          clade_relation = CladeRelation.new
          parse_attributes(clade_relation, ["id_ref_0", "id_ref_1", "distance", "type"])

          #@ add unit test for this
          if not @reader.empty_element?
            @reader.read
            if is_element?('confidence')
              clade_relation.confidence = parse_confidence
            end
          end
          tree.clade_relations << clade_relation

        when 'sequence_relation'
          sequence_relation = SequenceRelation.new
          parse_attributes(sequence_relation, ["id_ref_0", "id_ref_1", "distance", "type"])
          if not @reader.empty_element?
            @reader.read
            if is_element?('confidence')
              sequence_relation.confidence = parse_confidence
            end
          end
          tree.sequence_relations << sequence_relation
        when 'phylogeny'
          #do nothing
        else
          tree.other << parse_other
          #puts "Not recognized element. #{@reader.name}"
        end
      end
    end
    # go to next element        
    @reader.read    
  end #end while not </phylogeny>
  #move on to the next tag after /phylogeny which is text, since phylogeny
  #end tag is empty element, which value is nil, therefore need to move to
  #the next meaningful element (therefore @reader.read twice)
  @reader.read 
  @reader.read

  return tree
end

Private Instance Methods

_schema() click to toggle source

(private) returns PhyloXML schema

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 230
def _schema
  XML::Schema.document(XML::Document.file(File.join(File.dirname(__FILE__),'phyloxml.xsd')))
end
_secure_filename(filename) click to toggle source

(private) It seems that LibXML::XML::Reader reads from the network even if LibXML::XML::Parser::Options::NONET is set. So, for URI-like filename, '://' is replaced with ':/'.

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 279
def _secure_filename(filename)
  # for safety, URI-like filename is checked.
  if /\A[a-zA-Z]+\:\/\// =~ filename then
    # for example, "http://a/b" is changed to "http:/a/b".
    filename = filename.sub(/\:\/\//, ':/')
  end
  filename
end
_skip_leader() click to toggle source

(private) loops through until reaches phylogeny stuff

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 290
def _skip_leader
  #loops through until reaches phylogeny stuff
  # Have to leave this way, if accepting strings, instead of files
  @reader.read until is_element?('phylogeny')
  nil
end
_validate(data_type, arg) click to toggle source

(private) do validation


Arguments:

  • (required) data_type_: :file for filename, :string for string

  • (required) arg: filename or string

Returns

(undefined)

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 241
def _validate(data_type, arg)
  options = { :options =>
    (LibXML::XML::Parser::Options::NOERROR |   # no error messages
     LibXML::XML::Parser::Options::NOWARNING | # no warning messages
     LibXML::XML::Parser::Options::NONET)      # no network access
  }
  case data_type
  when :file
    # No validation when special file e.g. FIFO (named pipe)
    return unless File.file?(arg)
    xml_instance = XML::Document.file(arg, options)
  when :string
    xml_instance = XML::Document.string(arg, options)
  else
    # no validation for unknown data type
    return
  end

  schema = _schema
  begin
    flag = xml_instance.validate_schema(schema) do |msg, flag|
      # The document of libxml-ruby says that the block is called
      # when validation failed, but it seems it is never called
      # even when validation failed!
      raise "Validation of the XML document against phyloxml.xsd schema failed. #{msg}"
    end
  rescue LibXML::XML::Error => evar
    raise "Validation of the XML document against phyloxml.xsd schema failed, or XML error occurred. #{evar.message}"
  end
  unless flag then
    raise "Validation of the XML document against phyloxml.xsd schema failed."
  end
end
has_reached_end_element?(str) click to toggle source
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 573
def has_reached_end_element?(str)
  if not(is_end_element?(str))        
    raise "Warning: Should have reached </#{str}> element here"
  end
end
is_element?(str) click to toggle source

Utility methods

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 565
def is_element?(str)
  @reader.node_type == XML::Reader::TYPE_ELEMENT and @reader.name == str ? true : false
end
is_end_element?(str) click to toggle source
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 569
def is_end_element?(str)
  @reader.node_type==XML::Reader::TYPE_END_ELEMENT and @reader.name == str ? true : false
end
parse_attributes(object, arr_of_attrs) click to toggle source

Parses list of attributes use for the code like: clade_relation.type = @reader

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 600
def parse_attributes(object, arr_of_attrs)
  arr_of_attrs.each do |attr|
    object.send("#{attr}=", @reader[attr])
  end
end
parse_clade_elements(current_node, current_edge) click to toggle source
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 606
def parse_clade_elements(current_node, current_edge)
  #no loop inside, loop is already outside

  if @reader.node_type == XML::Reader::TYPE_ELEMENT
    case @reader.name
    when 'branch_length'
      # @todo add unit test for this. current_edge is nil, if the root clade
      # has branch_length attribute. 
      @reader.read
      branch_length = @reader.value
      current_edge.distance = branch_length.to_f if current_edge != nil
      @reader.read
    when 'width'
      @reader.read
      current_node.width = @reader.value
      @reader.read
    when  'name'
      @reader.read
      current_node.name = @reader.value
      @reader.read
    when 'events'
      current_node.events = parse_events
    when 'confidence'
      current_node.confidences << parse_confidence
    when 'sequence'
      current_node.sequences << parse_sequence
    when 'property'
      current_node.properties << parse_property
    when 'taxonomy'
      current_node.taxonomies << parse_taxonomy
    when 'distribution'
      current_node.distributions << parse_distribution
    when 'node_id'
      id = Id.new
      id.type = @reader["type"]
      @reader.read
      id.value = @reader.value
      @reader.read
      #has_reached_end_element?('node_id')
      #@todo write unit test for this. There is no example of this in the example files
      current_node.id = id
    when 'color'
      color = BranchColor.new
      parse_simple_element(color, 'red')
      parse_simple_element(color, 'green')
      parse_simple_element(color, 'blue')
      current_node.color = color
      #@todo add unit test for this
    when 'date'
      date = Date.new
      date.unit = @reader["unit"]
      #move to the next token, which is always empty, since date tag does not
      # have text associated with it
      @reader.read
      @reader.read #now the token is the first tag under date tag
      while not(is_end_element?('date'))
        parse_simple_element(date, 'desc')
        parse_simple_element(date, 'value')
        parse_simple_element(date, 'minimum')
        parse_simple_element(date, 'maximum')
        @reader.read
      end
      current_node.date = date
    when 'reference'
      reference = Reference.new()
      reference.doi = @reader['doi']
      if not @reader.empty_element?
        while not is_end_element?('reference')
          parse_simple_element(reference, 'desc')
          @reader.read
        end
      end
      current_node.references << reference
    when 'binary_characters'
      current_node.binary_characters  = parse_binary_characters
    when 'clade'
      #do nothing
    else
      current_node.other << parse_other
      #puts "No match found in parse_clade_elements.(#{@reader.name})"
    end

  end

end
parse_events() click to toggle source
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 692
def parse_events()
  events = PhyloXML::Events.new
  @reader.read #go to next element
  while not(is_end_element?('events')) do
    parse_simple_elements(events, ['type', 'duplications',
                                        'speciations', 'losses'])
    if is_element?('confidence')
      events.confidence = parse_confidence
      #@todo could add unit test for this (example file does not have this case)
    end
    @reader.read
  end
  return events
end
parse_simple_element(object, name) click to toggle source

Parses a simple XML element. for example <speciations>1</speciations> It reads in the value and assigns it to object.speciation = 1 Also checks if have reached end tag (</speciations> and gives warning if not

# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 583
def parse_simple_element(object, name)
  if is_element?(name)
    @reader.read
    object.send("#{name}=", @reader.value)
    @reader.read
    has_reached_end_element?(name)
  end
end
parse_simple_elements(object, elements) click to toggle source
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 592
def parse_simple_elements(object, elements)
  elements.each do |elmt|
      parse_simple_element(object, elmt)
  end      
end
parse_taxonomy() click to toggle source
# File lib/bio/db/phyloxml/phyloxml_parser.rb, line 707
def parse_taxonomy
  taxonomy = PhyloXML::Taxonomy.new
  parse_attributes(taxonomy, ["id_source"])
  @reader.read
  while not(is_end_element?('taxonomy')) do

    if @reader.node_type == XML::Reader::TYPE_ELEMENT
      case @reader.name
      when 'code'
        @reader.read
        taxonomy.code = @reader.value
        @reader.read
      when 'scientific_name'
        @reader.read
        taxonomy.scientific_name = @reader.value
        @reader.read
      when 'rank'
        @reader.read
        taxonomy.rank = @reader.value
        @reader.read
      when 'authority'
        @reader.read
        taxonomy.authority = @reader.value
        @reader.read
      when 'id'
        taxonomy.taxonomy_id = parse_id('id')
      when 'common_name'
        @reader.read
        taxonomy.common_names << @reader.value
        @reader.read
        #has_reached_end_element?('common_name')
      when 'synonym'
        @reader.read
        taxonomy.synonyms << @reader.value
        @reader.read
        #has_reached_end_element?('synonym')
      when 'uri'
        taxonomy.uri = parse_uri
      else
        taxonomy.other << parse_other
      end
    end

    @reader.read  #move to next tag in the loop
  end