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Contents
#!/usr/bin/env ruby
# NOTE make sure the newick has no spaces for jsPhyloXML
# NOTE for Archaeopteryx, you need <name>#{boot}</name> to show
# bootsraps, but for jsPhyloXML, just the confidence is needed
require "set"
require "bio"
def leaf? tree, node
tree.children(node).empty?
end
newick = ARGV.first
treeio = Bio::FlatFile.open(Bio::Newick, newick)
newick = treeio.next_entry
$tree = newick.tree
$xml_start = %q{<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
<phylogeny rooted="false">
<clade>
}
$xml_end = %q{</clade>
</phylogeny>
</phyloxml>
}
def leaf? tree, node
tree.descendents(node).count.zero?
end
def make_xml_string descendents, start_node
while (node = descendents.shift)
unless $already_added.include? node
if leaf? $tree, node
# TODO this will raise something if no dist, rescue it
dist = $tree.distance(start_node, node)
$xml_start << "<clade>
<name>#{node.name}</name>
<branch_length>#{dist}</branch_length>
</clade>\n"
$already_added << node
$prev_node = node
else
boot = node.bootstrap
if boot
boot_xml = %Q{<confidence type="bootstrap">#{boot}</confidence>}
else
boot_xml = ""
end
# TODO this will raise something if no dist, rescue it
dist = $tree.distance(start_node, node)
$xml_start << "<clade>
<branch_length>#{dist}</branch_length>
#{boot_xml}"
STDERR.puts "LOG -- recurse"
make_xml_string $tree.descendents(node), node
$xml_start << "</clade>\n"
$already_added << node
end
end
end
end
$already_added = Set.new
STDERR.puts $tree.nodes.inspect
start_node = $tree.root
$descendents = $tree.descendents(start_node)
STDERR.puts $descendents.inspect
make_xml_string $descendents, start_node
puts $xml_start
puts "#{$xml_end}"
Version data entries
31 entries across 31 versions & 1 rubygems