Difference between revisions of "BioRuby PhyloXML HowTo documentation"

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m (How to parse a file)
m (How to parse a file)
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=How to parse a file=
 
=How to parse a file=
 
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<code>
<nowiki>  
 
 
  require 'bio'
 
  require 'bio'
  
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   puts tree.name
 
   puts tree.name
 
  end
 
  end
</nowiki>
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</code>

Revision as of 20:43, 11 August 2009

Intro

PhyloXML is a tree format for saving and exchanging data of annotated phylogenetic trees. PhyloXML parsers and writers are implemented in BioRuby, BioPython and BioPerl. More information at www.phyloxml.org

Requirements

In addition to BioRuby library you need a libxml ruby bindings. To install:

gem install -r libxml-ruby

How to parse a file

require 'bio'
# Create new phyloxml parser
phyloxml = Bio::PhyloXML::Parser.new('example.xml')
# Print the names of all trees in the file
phyloxml.each do |tree|
  puts tree.name
end