Class: Bio::AssemblyGraphAlgorithms::AcyclicConnectionFinder

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

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#calibrate_distance_accounting_for_probes(finishm_graph, probe1_index, probe2_index, distance) ⇒ Object

Algorithms like SingleCoherentWanderer#wander give an overly short base pair distance between two probes, because the length of the node containing the probe at either end is not included in the calculation.

Return the calibrated distance i.e. the true base pair distance between the start of each node pair. Returned is the given distance plus the distance between the start of each probe and the end of the containing node.



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# File 'lib/assembly/acyclic_connection_finder.rb', line 55

def calibrate_distance_accounting_for_probes(finishm_graph, probe1_index, probe2_index, distance)
  read1 = finishm_graph.probe_node_reads[probe1_index]
  read2 = finishm_graph.probe_node_reads[probe2_index]
  probe_node1 = finishm_graph.probe_nodes[probe1_index]
  probe_node2 = finishm_graph.probe_nodes[probe2_index]

  # If the start and end nodes are the same, that's a special case:
  if finishm_graph.probe_nodes[probe1_index].node_id == finishm_graph.probe_nodes[probe2_index].node_id
    if (read1.direction == true and read2.direction == false) or
      (read1.direction == false and read2.direction == true)
      return probe_node1.length - read1.offset_from_start_of_node - read2.offset_from_start_of_node - finishm_graph.graph.hash_length
    else
      raise "Programming error: to connect within a single contig two probes must have opposite directions: found #{read1.direction} and #{read2.direction}"
    end
  else
    # Usual case - start and end nodes are different nodes
    to_return = distance
    # add the first probe side
    to_return += probe_node1.length-read1.offset_from_start_of_node-finishm_graph.graph.hash_length
    # add the second probe side
    to_return += probe_node2.length-read1.offset_from_start_of_node-finishm_graph.graph.hash_length
    return to_return
  end
end

#find_trails_between_nodes(graph, initial_oriented_node, terminal_oriented_node, leash_length, options = {}) ⇒ Object

Find trails between two oriented nodes, both facing the same way along the path.

Options:

  • :recoherence_kmer: use a longer kmer to help de-bubble and de-cicularise (default don’t use this)

  • :sequences: Bio::Velvet::Sequence object holding sequences of nodes within leash length



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# File 'lib/assembly/acyclic_connection_finder.rb', line 35

def find_trails_between_nodes(graph, initial_oriented_node, terminal_oriented_node, leash_length, options={})

  #TODO: this is now implemented in the finishm_graph object - just get it from there
  initial_path = Bio::Velvet::Graph::OrientedNodeTrail.new
  initial_path.add_oriented_node initial_oriented_node

  finder = Bio::AssemblyGraphAlgorithms::SingleCoherentPathsBetweenNodesFinder.new
  return finder.find_all_connections_between_two_nodes(
    graph, initial_path, terminal_oriented_node, leash_length, options[:recoherence_kmer], options[:sequences], options
    )
end