Class: Bio::PhyloXML::Parser

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

Overview

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

Defined Under Namespace

Classes: ClosedPhyloXMLParser

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(str, validate = true) ⇒ Parser

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 Bio::PhyloXML::Parser.open(filename).

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



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# File 'lib/bio/phyloxml/parser.rb', line 317

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

Instance Attribute Details

#other ⇒ Object (readonly)

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



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

def other
  @other
end

Class Method Details

.for_io(io, validate = true) ⇒ Object

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



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# File 'lib/bio/phyloxml/parser.rb', line 217

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

.open(filename, validate = true) ⇒ Object

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



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# File 'lib/bio/phyloxml/parser.rb', line 101

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) ⇒ Object

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



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# File 'lib/bio/phyloxml/parser.rb', line 142

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

Instance Method Details

#[](i) ⇒ Object

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]



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# File 'lib/bio/phyloxml/parser.rb', line 363

def [](i)
  tree = nil
  (i+1).times do
   tree =  self.next_tree
  end
  return tree
end

#close ⇒ Object

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

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

Returns

nil



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# File 'lib/bio/phyloxml/parser.rb', line 187

def close
  @reader.close
  @reader = ClosedPhyloXMLParser.new
  nil
end

#closed? ⇒ Boolean

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

Returns

true or false

Returns:

  • (Boolean) 


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# File 'lib/bio/phyloxml/parser.rb', line 197

def closed?
  if @reader.kind_of?(ClosedPhyloXMLParser) then
    true
  else
    false
  end
end

#each ⇒ Object

Iterate through all trees in the file.

phyloxml = Bio::PhyloXML::Parser.open('example.xml')
phyloxml.each do |tree|
  puts tree.name
end



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# File 'lib/bio/phyloxml/parser.rb', line 350

def each
  while tree = next_tree
    yield tree
  end
end

#next_tree ⇒ Object

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 PhyloXML::Parser#other.

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

Bio::PhyloXML::Tree



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# File 'lib/bio/phyloxml/parser.rb', line 380

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