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# Bio::KEGG::Taxonomy

## Description

Parse the KEGG 'taxonomy' file which describes taxonomic classification of organisms.

## References

The KEGG 'taxonomy' file is available at

- ftp.genome.jp/pub/kegg/genes/taxonomy

### Attributes

leaves[R]
path[R]
root[RW]
tree[R]

### Public Class Methods

new(filename, orgs = []) click to toggle source

    # File lib/bio/db/kegg/taxonomy.rb, line 26
    def initialize(filename, orgs = [])
      # Stores the taxonomic tree as a linked list (implemented in Hash), so
      # every node need to have unique name (key) to work correctly
      @tree = Hash.new

      # Also stores the taxonomic tree as a list of arrays (full path)
      @path = Array.new

      # Also stores all leaf nodes (organism codes) of every intermediate nodes
      @leaves = Hash.new

      # tentative name for the root node (use accessor to change)
      @root = 'Genes'

      hier = Array.new
      level = 0
      label = nil

      File.open(filename).each do |line|
        next if line.strip.empty?

        # line for taxonomic hierarchy (indent according to the number of # marks)
        if line[/^#/]
          level = line[/^#+/].length
          label = line[/[A-z].*/]
          hier[level] = sanitize(label)

        # line for organims name (unify different strains of a species)
        else
          tax, org, name, desc = line.chomp.split("\t")
          if orgs.nil? or orgs.empty? or orgs.include?(org)
            species, strain, = name.split('_')
            # (0) Grouping of the strains of the same species.
            #  If the name of species is the same as the previous line,
            #  add the species to the same species group.
            #   ex. Gamma/enterobacteria has a large number of organisms,
            #       so sub grouping of strains is needed for E.coli strains etc.
            #
            # However, if the species name is already used, need to avoid
            # collision of species name as the current implementation stores
            # the tree as a Hash, which may cause the infinite loop.
            #
            # (1) If species name == the intermediate node of other lineage
            #  Add '_sp' to the species name to avoid the conflict (1-1), and if
            #  'species_sp' is already taken, use 'species_strain' instead (1-2).
            #   ex. Bacteria/Proteobacteria/Beta/T.denitrificans/tbd
            #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_ATCC33889/tdn
            #    -> Bacteria/Proteobacteria/Beta/T.denitrificans/tbd
            #       Bacteria/Proteobacteria/Epsilon/T.denitrificans_sp/tdn
            #
            # (2) If species name == the intermediate node of the same lineage
            #  Add '_sp' to the species name to avoid the conflict.
            #   ex. Bacteria/Cyanobacgteria/Cyanobacteria_CYA/cya
            #       Bacteria/Cyanobacgteria/Cyanobacteria_CYB/cya
            #       Bacteria/Proteobacteria/Magnetococcus/Magnetococcus_MC1/mgm
            #    -> Bacteria/Cyanobacgteria/Cyanobacteria_sp/cya
            #       Bacteria/Cyanobacgteria/Cyanobacteria_sp/cya
            #       Bacteria/Proteobacteria/Magnetococcus/Magnetococcus_sp/mgm
            sp_group = "#{species}_sp"
            if @tree[species]
              if hier[level+1] == species
                # case (0)
              else
                # case (1-1)
                species = sp_group
                # case (1-2)
                if @tree[sp_group] and hier[level+1] != species
                  species = name
                end
              end
            else
              if hier[level] == species
                # case (2)
                species = sp_group
              end
            end
            # 'hier' is an array of the taxonomic tree + species and strain name.
            #  ex. [nil, Eukaryotes, Fungi, Ascomycetes, Saccharomycetes] +
            #      [S_cerevisiae, sce]
            hier[level+1] = species       # sanitize(species)
            hier[level+2] = org
            ary = hier[1, level+2]
            warn ary.inspect if $DEBUG
            add_to_tree(ary)
            add_to_leaves(ary)
            add_to_path(ary)
          end
        end
      end
      return tree
    end

### Public Instance Methods

add_to_leaves(ary) click to toggle source

Add a new path [node, subnode, subsubnode, ..., leaf] under the root node and stores leaf nodes to the every intermediate nodes as an Array.

    # File lib/bio/db/kegg/taxonomy.rb, line 140
    def add_to_leaves(ary)
      leaf = ary.last
      ary.each do |node|
        @leaves[node] ||= Array.new
        @leaves[node] << leaf
      end
    end

add_to_path(ary) click to toggle source

Add a new path [node, subnode, subsubnode, ..., leaf] under the root node and stores the path itself in an Array.

    # File lib/bio/db/kegg/taxonomy.rb, line 150
    def add_to_path(ary)
      @path << ary
    end

add_to_tree(ary) click to toggle source

Add a new path [node, subnode, subsubnode, ..., leaf] under the root node and every intermediate nodes stores their child nodes as a Hash.

    # File lib/bio/db/kegg/taxonomy.rb, line 129
    def add_to_tree(ary)
      parent = @root
      ary.each do |node|
        @tree[parent] ||= Hash.new
        @tree[parent][node] = nil
        parent = node
      end
    end

compact(node = root) click to toggle source

Compaction of intermediate nodes of the resulted taxonomic tree.

    - If child node has only one child node (grandchild), make the child of
      grandchild as a grandchild.
    ex.
      Plants / Monocotyledons / grass family / osa
      --> Plants / Monocotyledons / osa

    # File lib/bio/db/kegg/taxonomy.rb, line 161
    def compact(node = root)
      # if the node has children
      if subnodes = @tree[node]
        # obtain grandchildren for each child
        subnodes.keys.each do |subnode|
          if subsubnodes = @tree[subnode]
            # if the number of grandchild node is 1
            if subsubnodes.keys.size == 1
              # obtain the name of the grandchild node
              subsubnode = subsubnodes.keys.first
              # obtain the child of the grandchlid node
              if subsubsubnodes = @tree[subsubnode]
                # make the child of grandchild node as a chlid of child node
                @tree[subnode] = subsubsubnodes
                # delete grandchild node
                @tree[subnode].delete(subsubnode)
                warn "--- compact: #{subsubnode} is replaced by #{subsubsubnodes}" if $DEBUG
                # retry until new grandchild also needed to be compacted.
                retry
              end
            end
          end
          # repeat recurseively
          compact(subnode)
        end
      end
    end

dfs(parent, &block) click to toggle source

Traverse the taxonomic tree by the depth first search method under the given (root or intermediate) node.

    # File lib/bio/db/kegg/taxonomy.rb, line 224
    def dfs(parent, &block)
      if children = @tree[parent]
        yield parent, children
        children.keys.each do |child|
          dfs(child, &block)
        end
      end
    end

dfs_with_level(parent, &block) click to toggle source

Similar to the dfs method but also passes the current level of the nest to the iterator.

    # File lib/bio/db/kegg/taxonomy.rb, line 235
    def dfs_with_level(parent, &block)
      @level ||= 0
      if children = @tree[parent]
        yield parent, children, @level
        @level += 1
        children.keys.each do |child|
          dfs_with_level(child, &block)
        end
        @level -= 1
      end
    end

organisms(group) click to toggle source

    # File lib/bio/db/kegg/taxonomy.rb, line 123
    def organisms(group)
      @leaves[group]
    end

reduce(node = root) click to toggle source

Reduction of the leaf node of the resulted taxonomic tree.

    - If the parent node have only one leaf node, replace parent node
      with the leaf node.
    ex.
     Plants / Monocotyledons / osa
     --> Plants / osa

    # File lib/bio/db/kegg/taxonomy.rb, line 196
    def reduce(node = root)
      # if the node has children
      if subnodes = @tree[node]
        # obtain grandchildren for each child
        subnodes.keys.each do |subnode|
          if subsubnodes = @tree[subnode]
            # if the number of grandchild node is 1
            if subsubnodes.keys.size == 1
              # obtain the name of the grandchild node
              subsubnode = subsubnodes.keys.first
              # if the grandchild node is a leaf node
              unless @tree[subsubnode]
                # make the grandchild node as a child node
                @tree[node].update(subsubnodes)
                # delete child node
                @tree[node].delete(subnode)
                warn "--- reduce: #{subnode} is replaced by #{subsubnode}" if $DEBUG
              end
            end
          end
          # repeat recursively
          reduce(subnode)
        end
      end
    end

to_s() click to toggle source

Convert the taxonomic tree structure to a simple ascii art.

    # File lib/bio/db/kegg/taxonomy.rb, line 248
    def to_s
      result = "#{@root}\n"
      @tree[@root].keys.each do |node|
        result += ascii_tree(node, "  ")
      end
      return result
    end

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