phyloXML is an XML language for saving, analyzing and exchanging data of annotated phylogenetic trees. The phyloXML parser in BioRuby is implemented in Bio::PhyloXML::Parser, and its writer in Bio::PhyloXML::Writer. More information can be found at phyloxml.org.
This phyloXML code has historically been part of the core BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-phyloxml and many more plugins are available at biogems.info.
This code was originally written by Diana Jaunzeikare during the Google Summer of Code 2009 for the Implementing phyloXML support in BioRuby project with NESCent, mentored by Christian Zmasek et al. For details of development, see github.com/latvianlinuxgirl/bioruby and the BioRuby mailing list archives.
NOTE: this is currently in the repackaging process and is not yet released! Production users should use the phyloXML support provided with BioRuby for the time being.
bio-phyloxml uses libxml-ruby, which requires several C libraries and their headers to be installed:
With these installed, the
libxml-ruby gems should be installed
gem install -r bio libxml-ruby
gem install bio-phyloxml
Users who were previously using the phyloXML support in the core
BioRuby gem should be able to migrate to using this gem very
easily. Simply install the
bio-phyloxml gem as described below, and
require 'bio-phyloxml' to the relevant application code.
require 'bio-phyloxml' # 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
If there are several trees in the file, you can access the one you wish by specifying its index:
tree = phyloxml
You can use all Bio::Tree methods on the tree, since PhyloXML::Tree inherits from Bio::Tree. For example,
tree.leaves.each do |node| puts node.name end
PhyloXML files can hold additional information besides phylogenies at the end of the file. This info can be accessed through the 'other' array of the parser object.
phyloxml = Bio::PhyloXML::Parser.open('example.xml') while tree = phyloxml.next_tree # do stuff with trees end puts phyloxml.other
# 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)
Here is an example of how to retrieve the scientific name of the clades included in each tree.
require 'bio-phyloxml' phyloxml = Bio::PhyloXML::Parser.open('ncbi_taxonomy_mollusca.xml') phyloxml.each do |tree| tree.each_node do |node| print "Scientific name: ", node.taxonomies.scientific_name, "\n" end end
require 'bio' phyloxml = Bio::PhyloXML::Parser.open('phyloxml_examples.xml') while tree = phyloxml.next_tree #do something with the trees end p phyloxml.other puts "\n" #=> output is an object representation #Print in a readable way puts phyloxml.other.to_xml, "\n" #=>: # #<align:alignment xmlns:align="http://example.org/align"> # <seq name="A">acgtcgcggcccgtggaagtcctctcct</seq> # <seq name="B">aggtcgcggcctgtggaagtcctctcct</seq> # <seq name="C">taaatcgc--cccgtgg-agtccc-cct</seq> #</align:alignment> #Once we know whats there, lets output just sequences phyloxml.other.children.each do |node| puts node.value end #=> # #acgtcgcggcccgtggaagtcctctcct #aggtcgcggcctgtggaagtcctctcct #taaatcgc--cccgtgg-agtccc-cct
The API doc is online. (TODO: generate and link) For more code examples see the test files in the source tree.
Information on the source tree, documentation, examples, issues and how to contribute, see
The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
If you use this software, please cite one of
- BioRuby: bioinformatics software for the Ruby programming language
- Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
This Biogem is published at #bio-phyloxml
Copyright (c) 2009 Diana Jaunzeikare. See LICENSE.txt for further details.