Module: IrokiLib::Main

Defined in:

lib/iroki_lib/main/main.rb

Class Method Summary

• .main(color_branches: nil, color_taxa_names: nil, exact: nil, remove_bootstraps_below: nil, color_map_f: nil, name_map_f: nil, auto_color: nil, display_auto_color_options: nil, newick_f: nil, out_f: nil) ⇒ Object

Class Method Details

.main(color_branches: nil, color_taxa_names: nil, exact: nil, remove_bootstraps_below: nil, color_map_f: nil, name_map_f: nil, auto_color: nil, display_auto_color_options: nil, newick_f: nil, out_f: nil) ⇒ Object

# File 'lib/iroki_lib/main/main.rb', line 23

def self.main(color_branches: nil,
              color_taxa_names: nil,
              exact: nil,
              remove_bootstraps_below: nil,
              color_map_f: nil,
              name_map_f: nil,
              auto_color: nil,
              display_auto_color_options: nil,
              newick_f: nil,
              out_f: nil)



  if display_auto_color_options
    puts "\n  Choices for --auto-color ..."
    print "  basic, basic_light, basic_dark, funky, funky_light, " +
          "funky_dark\n\n"
    exit
  end

  auto_color_options =
    ["basic", "basic_light", "basic_dark",
     "funky", "funky_light", "funky_dark",]


  if(!auto_color.nil? &&
     !auto_color_options.include?(auto_color))
    puts "\n  Choices for --auto-color ..."
    print "  basic, basic_light, basic_dark, funky, funky_light, " +
          "funky_dark\n\n"

    Trollop.die :auto_color, "#{auto_color} is not a valid option"
  end

  case auto_color
  when nil
    auto_colors = BASIC
  when "basic"
    auto_colors = BASIC
  when "basic_light"
    auto_colors = BASIC_LIGHT
  when "basic_dark"
    auto_colors = BASIC_DARK
  when "funky"
    auto_colors = FUNKY
  when "funky_light"
    auto_colors = FUNKY_LIGHT
  when "funky_dark"
    auto_colors = FUNKY_DARK
  end

  # color_branches = true
  # color_taxa_names = true
  # exact = false
  # color_map_f = "test_files/500.patterns_with_name_map"
  # name_map_f = "test_files/500.name_map"
  # ARGV[0] = "test_files/500.zetas.tre"
  newick = check_file newick_f, :newick

  color_f = nil
  if color_taxa_names || color_branches
    color_f = check_file color_map_f, :color_map_f
  end

  check = color_map_f &&
          !color_taxa_names &&
          !color_branches

  abort_if check,
           "A pattern file was provided without specifying " +
           "any coloring options"


  # if passed color other than one defined, return black
  black = "#000000"
  red = "#FF1300"
  yellow = "#FFD700"
  blue = "#5311FF"
  green = "#00FF2C"
  color2hex = Hash.new "[&!color=\"#{black}\"]"
  color2hex.merge!({
                     "black" => "[&!color=\"#{black}\"]",
                     "red" => "[&!color=\"#{red}\"]",
                     "blue" => "[&!color=\"#{blue}\"]",
                     "yellow" => "[&!color=\"#{yellow}\"]",
                     "green" => "[&!color=\"#{green}\"]"
                   })

  # check if complementary colors requested
  if color_f
    colors = Set.new
    File.open(color_f).each_line do |line|
      _, color = line.chomp.split "\t"

      colors << color
    end

    auto_color = colors.all? { |color| color.match /\A[0-4]\Z/ }
  end

  # get the color patterns
  if color_f
    patterns = {}
    File.open(color_f).each_line do |line|
      pattern, color = line.chomp.split "\t"

      color = "black" if color.nil? || color.empty?

      if name_map_f || color_taxa_names || color_branches
        pattern = clean_name pattern
      end

      if !exact
        pattern = Regexp.new pattern
      end

      if auto_color
        patterns[pattern] = "[&!color=\"#{auto_colors[color]}\"]"
      else
        if hex? color
          patterns[pattern] = "[&!color=\"#{color}\"]"
        else
          patterns[pattern] = color2hex[color]
        end
      end
    end
  end

  treeio = Bio::FlatFile.open(Bio::Newick, newick)

  newick = treeio.next_entry
  tree = newick.tree

  # do this first cos everything after will use the "new" names
  if name_map_f
    name_map = parse_name_map name_map_f

    tree.collect_node! do |node|
      unless node.name.nil?
        # every name is cleaned no matter what
        node.name = clean node.name

        if name_map.has_key?(node.name)
          node.name = name_map[node.name]
        end
      end

      node
    end
  end

  if color_taxa_names
    leaves = tree.leaves.map do |n|
      name = clean_name n.name

      if (color = add_color_to_leaf_branch(patterns, name, exact))
        name + color
      else
        name
      end
    end
  else
    leaves = tree.leaves.map { |n| clean_name n.name }
  end

  if color_branches
    total = tree.nodes.count
    n = 0
    tree.collect_node! do |node|
      n += 1
      $stderr.printf "Node: %d of %d\r", n, total

      color_nodes patterns, tree, node, exact
    end
  end
  $stderr.puts

  if remove_bootstraps_below
    tree.collect_node! do |node|
      if node.bootstrap && node.bootstrap < remove_bootstraps_below
        node.bootstrap_string = ""
      end

      node
    end
  end



  tre_str = tree.newick(indent: false).gsub(/'/, '')

  nexus = "#NEXUS
begin taxa;
dimensions ntax=#{leaves.count};
taxlabels
#{leaves.join("\n")}
;
end;

begin trees;
  tree tree_1 = [&R] #{tre_str}
end;

#{FIG}"

  File.open(out_f, "w") { |f| f.puts nexus }
end