Class: Bio::AssemblyGraphAlgorithms::Fluffer

Inherits:
Object
  • Object
show all
Includes:
FinishM::Logging
Defined in:
lib/assembly/fluffer.rb

Defined Under Namespace

Classes: FlufferHalfResult, FlufferPathSet

Constant Summary collapse

BEYOND_LEASH_LENGTH_FATE = 
:beyond_leash_length
TERMINAL_NODE_FATE = 
:terminal_node
DEAD_END_FATE = 
:dead_end

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#fluff(finishm_graph, leash_length, options = {}) ⇒ Object

Return an array of array of paths.



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# File 'lib/assembly/fluffer.rb', line 32

def fluff(finishm_graph, leash_length, options={})
  log.debug "Fluffing part 1.." if log.debug?
  half_results = fluff_part1(finishm_graph, leash_length, options)

  log.debug "Found fluff half results: #{half_results}" if log.debug?
  log.debug "Fluffing part 2.." if log.debug?
  return fluff_part2(half_results)
end

#fluff_part1(finishm_graph, leash_length, options = {}) ⇒ Object 



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# File 'lib/assembly/fluffer.rb', line 41

def fluff_part1(finishm_graph, leash_length, options={})
  # Get a set of all probes so that they can be checked against
  log.debug "Found #{finishm_graph.probe_nodes.reject{|node| node.nil?}.length} different probes that were in the final velvet graph" if log.debug?
  half_results = []
  graph = finishm_graph.graph

  # For each probe in the graph
  finishm_graph.probe_nodes.each_with_index do |node, probe_index|

    # If the node is not found in the graph, then forget it
    if node.nil?
      half_results.push FlufferHalfResult.new

    else # probe was found in the graph. Start finding them paths.
      # start exploring the squid way
      golden_paths = [] #These is the full paths found
      golden_fragments = [] #paths to join up to the end
      already_visited_nodes = Set.new #Nodes that have already been explored
      golden_path_fates = [] #An array of how each of the paths were halted

      golden_onodes = Set.new #Nodes that stop exploration
      terminal_nodes = Set.new
      # Add all the nodes that are being probed, because we don't want double exploration
      # i.e. want probe1 => probe2, probe2 => probe3, but not probe1 => probe2 => probe3
      finishm_graph.probe_nodes.each_with_index do |node, probe_index2|
        # Don't add the node itself. This is a special case which is already handled below
        unless probe_index == probe_index2 or node.nil?
          terminal_nodes << finishm_graph.velvet_oriented_node(probe_index2).to_settable
        end
      end

      stack = DS::Stack.new
      stack.push finishm_graph.initial_path_from_probe(probe_index)

      while current_path = stack.pop
        log.debug "Perhaps #{current_path}?" if log.debug?
        if golden_onodes.include?(current_path.last.to_settable)
          # Probably a golden fragment, unless the node found is in the current path.
          # if that is true, that's a loop along a golden path.
          first_index = nil
          current_path.each_with_index do |directed_node, i|
            if directed_node.node == current_path.last.node and
              directed_node.first_side == current_path.last.first_side
              first_index = i
              break
            end
          end

          if first_index == current_path.length-1
            # Found another golden path(s)
            log.debug "Ran into a golden node" if log.debug?
            golden_fragments.push current_path
            current_path.each do |onode|
              golden_onodes << onode.to_settable
            end
          else
            # Loop found along a golden path or fragment
            log.debug "Found a loop along a golden path: #{current_path}" if log.debug?
            next
          end
        elsif already_visited_nodes.include?(current_path.last.to_settable) and
          !terminal_nodes.include?(current_path.last.to_settable)
          # Already seen this (non-golden) node, do nothing with it
          log.debug "Skipping #{current_path.last} since that has already been seen" if log.debug?
          next
        else
          if log.debug?
            second_last_node = current_path[current_path.length-2]
            second_last_node ||= 'initial_node'
            log.debug "That's a new node, #{second_last_node}/#{current_path.last}" if log.debug?
          end

          # if we aren't beyond the leash. Presumably this
          # doesn't happen much, but there is a possibility that the leash will
          # prevent a real path being discovered. If there is two or more paths to a node
          # and a path longer than the leash is discovered first, then all the
          # nodes on that leash will be marked as discovered when they really aren't
          # TODO: fix the above bug
          if leash_length.nil? or current_path.length_in_bp < leash_length
            # Found a new node for the user to play with
            already_visited_nodes << current_path.last.to_settable

            # Have we found a path to one of the other probes?
            if terminal_nodes.include?(current_path.last.to_settable)
              log.debug "Found the terminal node: #{current_path}" if log.debug?
              golden_paths.push current_path
              golden_path_fates.push TERMINAL_NODE_FATE

            else # Use an else statement here because we want exploration to stop when other probes are encountered

              # prep for next time
              # Sort node IDs to simplify testing
              next_nodes = current_path.neighbours_of_last_node(graph).sort{|n1, n2|
                -(n1.node.node_id <=> n2.node.node_id)
              }
              next_nodes.each do |n|
                path = current_path.copy
                path.add_oriented_node n
                log.debug "Pushing a path yet to be explored: #{path}" if log.debug?
                stack.push path
              end

              # If we are at a dead end, add this whole path as a golden path. This
              # is low coverage fluff, perhaps. Or it is nothing.
              if next_nodes.empty?
                log.debug "Found a dead end path: #{current_path}" if log.debug?
                golden_paths.push current_path
                golden_path_fates.push DEAD_END_FATE
                current_path.each do |onode|
                  golden_onodes << onode.to_settable
                end
              end
            end
          else
            if log.debug?
              log.debug "Found a path that made it to the end of the leash, with path length #{current_path.length_in_bp} vs leash length #{leash_length}"
              log.debug "Path given up on: #{current_path}"
              log.debug "Path sequence given up on: #{current_path.sequence}"
              log.debug "Node lengths: #{current_path.collect{|n| n.node.length_alone}.join(',')}"
            end
            # Record this past-leash-length path
            golden_paths.push current_path
            golden_path_fates.push BEYOND_LEASH_LENGTH_FATE
            current_path.each do |onode|
              golden_onodes << onode.to_settable
            end
          end
        end
      end

      log.debug "Found #{golden_paths.length} golden paths and #{golden_fragments.length} golden fragments" if log.debug?
      fluff_half_result = FlufferHalfResult.new
      fluff_half_result.golden_paths = golden_paths
      fluff_half_result.golden_path_fragments = golden_fragments
      fluff_half_result.golden_path_fates = golden_path_fates

      half_results.push fluff_half_result
    end
  end

  return half_results
end

#fluff_part2(half_results) ⇒ Object 



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# File 'lib/assembly/fluffer.rb', line 184

def fluff_part2(half_results)
  all_all_paths = []

  half_results.each do |segment_half_result|
    # OK, so we've transformed the data into a state where there is
    # at least one path through the data
    # and tentacles hanging off various golden nodes.
    # Now separate out the paths and return the array.
    # First transform the data so it can be referenced by the end node
    terminal_golden_nodes_to_paths = {}
    segment_half_result.golden_path_fragments.each do |fragment|
      l = fragment.last.to_settable
      terminal_golden_nodes_to_paths[l] ||= []
      terminal_golden_nodes_to_paths[l].push fragment
    end
    # Next backtrack through the paths
    # Each path starts at the beginning and ends at a
    # golden node
    all_paths = FlufferPathSet.new
    stack = DS::Stack.new
    # Push the golden path and all paths that finish at the last node
    segment_half_result.golden_paths.each_with_index do |golden_path, i|
      stack.push [golden_path, 0, segment_half_result.golden_path_fates[i]]
    end

    while array = stack.pop
      current_path = array[0]
      num_to_ignore = array[1]
      fate = array[2]

      log.debug "Defragging #{current_path.to_s}/#{fate}, ignoring the last #{num_to_ignore} nodes" if log.debug?
      all_paths.push current_path
      all_paths.fates.push fate

      # Iterate down this path, spawning new paths if there
      # are paths that intersect
      passed_nodes = []
      current_path.trail.reverse.each_with_index do |onode, i|
        unless i < num_to_ignore #ignore the last one(s) because they've already been handled
          frags = terminal_golden_nodes_to_paths[onode.to_settable]
          log.debug "Offshoots from #{onode}: #{frags.nil? ? '[]' : frags.collect{|f| f.collect{|n| n.node_id}.join(',')}.join(' and ')}" if log.debug?
          if frags
            frags.each do |fragment|
              log.debug "Using an offshoot: #{fragment.to_s}" if log.debug?
              # The fragment extends from the beginning to the golden node,
              # the current node. So create a new complete path,
              # And push it to the stack.
              new_golden = fragment.copy
              log.debug "Adding #{new_golden.to_s} and #{passed_nodes.collect{|n| n.node_id}}" if log.debug?
              passed_nodes.reverse.each_with_index do |onode, i|
                new_golden.add_oriented_node onode
              end
              log.debug "Enqueueing: #{new_golden.to_s} ignoring the last #{i+1} nodes" if log.debug?
              stack.push [new_golden, i+1, fate]
            end
          end
        end
        passed_nodes.push onode
      end
    end

    # All the paths are in an array, just a linear series of distinct paths
    all_all_paths.push all_paths
  end

  return all_all_paths
end