Module: Dphil::NewickTree

Defined in:
lib/dphil/newick.rb

Class Method Summary collapse

Class Method Details

.tree_from_nex(filename, tree_id: nil, taxa_map: nil) ⇒ Object

rubocop:disable MethodLength



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# File 'lib/dphil/newick.rb', line 9

def tree_from_nex(filename, tree_id: nil, taxa_map: nil) # rubocop:disable MethodLength
  data = File.read(filename).to_s[/^\s*tree MajRule = \[&R\](.*)$/, 1]
  tree = Bio::Newick.new(data).tree
  new_taxa_id = (taxa_map&.keys&.max || 0) + 1
  tree_hsh = tree.nodes.each_with_object({}) do |n, acc|
    next if n == tree.root
    id = taxa_map&.key(n.name)
    if id.nil?
      id = new_taxa_id
      new_taxa_id += 1
    end
    acc[id] = n
  end

  tree_nodes = tree_hsh.each_with_object({}) do |(id, node), acc|
    out = {
      id: id,
      name: node.name || "##{id}",
    }

    parent = tree.parent(node)
    out[:parent] = tree_hsh.key(parent) || 0
    out[:length] = tree.get_edge(node, parent)&.distance

    out[:children] = tree.children(node).map do |n|
      tree_hsh.key(n)
    end
    acc[id] = out
  end

  stats = {
    length: nil,
    ci: nil,
    hi: nil,
    ci_ex: nil,
    hi_ex: nil,
    ri: nil,
    rc: nil,
  }

  Dphil::Tree.new(tree_id, nodes: tree_nodes, stats: stats)
end