Class: Bio::FinishM::PathCounter

Inherits:
Object
  • Object
show all
Includes:
Logging
Defined in:
lib/finishm/path_counter.rb

Instance Method Summary collapse

Methods included from Logging

#log

Instance Method Details

#add_options(optparse_object, options) ⇒ Object 



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# File 'lib/finishm/path_counter.rb', line 4

def add_options(optparse_object, options)
  options.merge! Bio::FinishM::Visualise::DEFAULT_OPTIONS
  optparse_object.banner = "\nUsage: finishm count_paths --assembly-???

  Count paths through assembly graph
  \n\n"

  optparse_object.separator "Input genome information"
  optparse_object.separator "\nIf an assembly is to be done, there must be some definition of reads:\n\n" #TODO improve this help
  Bio::FinishM::ReadInput.new.add_options(optparse_object, options)

  optparse_object.separator "\nOptional graph-exploration arguments:\n\n"
  Bio::FinishM::Visualise.new.add_probe_options(optparse_object, options)

  optparse_object.separator "\nOptional graph-related arguments:\n\n"
  Bio::FinishM::GraphGenerator.new.add_options(optparse_object, options)
end

#count_paths_through_graph(finishm_graph, initial_onodes, options = {}) ⇒ Object 



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# File 'lib/finishm/path_counter.rb', line 81

def count_paths_through_graph(finishm_graph, initial_onodes, options={})
  height_finder = Bio::AssemblyGraphAlgorithms::HeightFinder.new

  by_height, = height_finder.traverse(finishm_graph.graph, initial_onodes, options)
  min_paths_through = height_finder.min_paths_through(by_height)
  max_paths_through = height_finder.max_paths_through(by_height)
  puts "Minimum number of distinct sequences to explain graph, assuming no errors: #{min_paths_through}."
  puts "Maximum number of distinct sequences allowed by graph: #{max_paths_through}."
end

#get_leash_start_nodes(finishm_graph, nodes_within_leash) ⇒ Object 



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# File 'lib/finishm/path_counter.rb', line 67

def get_leash_start_nodes(finishm_graph, nodes_within_leash)
  log.info "Finding nodes from which to begin search.."
  start_onodes, = Bio::AssemblyGraphAlgorithms::HeightFinder.new.find_oriented_edge_of_range(finishm_graph.graph, nodes_within_leash)
  if start_onodes.empty?
    #possible with a completely cyclic graph, choose any node to begin
    onode = Bio::Velvet::Graph::OrientedNodeTrail::OrientedNode finishm_graph.graph.nodes[1], true
    start_onodes = [onode]
    log.info "Graph appears to be a self-contained loop, so chose an arbitrary  node"
  else
    log.info "Found #{start_onodes.length} nodes"
  end
  return start_onodes
end

#run(options, argv) ⇒ Object 



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# File 'lib/finishm/path_counter.rb', line 31

def run(options, argv)
  read_input = Bio::FinishM::ReadInput.new
  read_input.parse_options options

  visualise = Bio::FinishM::Visualise.new

  if options[:interesting_probes] or options[:interesting_probe_names]
    finishm_graph, interesting_node_ids, = visualise.generate_graph_from_probes(read_input, options)
    if options[:probe_to_node_map]
      # Output probe map if asked
      visualise.write_probe_to_node_map(options[:probe_to_node_map], finishm_graph, options[:interesting_probes])
    end
  elsif options[:interesting_nodes]
    finishm_graph = visualise.generate_graph_from_nodes(read_input, options)
    interesting_nodes = options[:interesting_nodes]
  elsif options[:assembly_files]
    finishm_graph, interesting_node_ids, = visualise.generate_graph_from_assembly(read_input, options)
  else
    finishm_graph = Bio::FinishM::GraphGenerator.new.generate_graph([], read_input, options)
  end


  if options[:graph_search_leash_length]
    # get a list of the nodes to be visualised given the leash length
    nodes_within_leash, node_ids_at_leash = visualise.get_nodes_within_leash(finishm_graph, interesting_node_ids, options)
    log.info "Found #{node_ids_at_leash.length} nodes at the end of the #{options[:graph_search_leash_length] }bp leash"
  else
    nodes_within_leash = finishm_graph.graph.nodes
  end

  initial_onodes = get_leash_start_nodes(finishm_graph, nodes_within_leash)

  log.info "Counting paths through assembly graph.."
  count_paths_through_graph(finishm_graph, initial_onodes,  :range => nodes_within_leash )
end

#validate_options(options, argv) ⇒ Object 



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# File 'lib/finishm/path_counter.rb', line 22

def validate_options(options, argv)
  #TODO: give a better description of the error that has occurred
  #TODO: require reads options
  visualise = Bio::FinishM::Visualise.new
  return visualise.validate_argv_length(argv) ||
    visualise.validate_probe_options(options) ||
    visualise.validate_assembly_options(options)
end