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No matching classes.

# 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 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

    # 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) 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) 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 Bio::PhyloXML::Parser.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() 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 PhyloXML::Parser#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

[Validate]

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