Class: Bio::FinishM::ORFsFinder

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

Constant Summary collapse

DEFAULT_OPTIONS = 
{
:min_orf_length => 96
}

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/orfs_finder.rb', line 8

def add_options(optparse_object, options)
  options.merge! Bio::FinishM::Visualise::DEFAULT_OPTIONS
  options.merge! DEFAULT_OPTIONS
  optparse_object.banner = "\nUsage: finishm find_orfs [--orf-amino-acids OUTPUT_FAA --orf-nucleotides OUTPUT_FNA]

  Find possible open reading frames in assembly graph
  \n\n"

  optparse_object.separator "\nOutput sequence files\n\n"
  optparse_object.on("--orf-amino-acids OUTPUT_FAA", "Output ORF amino acid sequences [default: orf.faa unless --orf-nucleotides is specified]") do |arg|
    options[:output_faa] = arg
  end
  optparse_object.on("--orf-nucleotides OUTPUT_FNA", "Output ORF nucleotide sequences [default: orf.fna unless --orf-amino-acids is specified]") do |arg|
    options[:output_fna] = arg
  end

  optparse_object.separator "\nInput 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 arguments:\n\n"
  optparse_object.on("--min-orf-length", "Minimum ORF length [default: 96]") do |arg|
    length = arg.to_i
    if length.to_s != arg or length.nil? or length < 1
      raise "Unable to parse minimum orf length parameter #{arg}, cannot continue"
    end
    options[:min_orf_length] = length
  end


  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

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



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# File 'lib/finishm/orfs_finder.rb', line 94

def find_orfs_in_graph(finishm_graph, initial_onodes, options={})
  initial_paths = initial_onodes.collect do |onode|
    path = Bio::Velvet::Graph::OrientedNodeTrail.new
    path.add_oriented_node onode
    path
  end

  orfer = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
  orf_trails = orfer.find_orfs_in_graph(finishm_graph.graph, initial_paths,
      options[:min_orf_length], options[:range])

  orfer.orf_sequences_from_trails(orf_trails, options[:min_orf_length])
end

#orf_to_settable(path, start_index, start_offset, end_index, end_offset) ⇒ Object 



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# File 'lib/finishm/orfs_finder.rb', line 127

def orf_to_settable(path, start_index, start_offset, end_index, end_offset)
  [path[start_index..end_index].collect{|onode| onode.to_settable},[start_offset, end_offset]]
end

#run(options, argv) ⇒ Object 



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# File 'lib/finishm/orfs_finder.rb', line 52

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)
  elsif options[:interesting_nodes]
    finishm_graph = visualise.generate_graph_from_nodes(read_input, options)
    interesting_node_ids = 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]
    #log.info "Finding nodes within the leash length of #{options[:graph_search_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" if options[:graph_search_leash_length]

    options[:range] = nodes_within_leash
  else
    options[:range] = finishm_graph.graph.nodes
  end

  initial_onodes = Bio::FinishM::PathCounter.new.get_leash_start_nodes(finishm_graph, options[:range])
  orfs = find_orfs_in_graph(finishm_graph, initial_onodes, options)
  log.info "Found #{orfs.length} open reading frames longer than #{options[:min_orf_length]}."
  if not options[:output_fna] and not options[:output_faa]
      options[:output_fna] = 'orfs.fna'
  end

  if options[:output_fna]
      write_orfs_to_file(orfs, options[:output_fna])
  end
  if options[:output_faa]
      write_orfs_to_file(orfs, options[:output_faa], translate=true)
  end
end

#validate_options(options, argv) ⇒ Object 



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# File 'lib/finishm/orfs_finder.rb', line 45

def validate_options(options, argv)
  visualise = Bio::FinishM::Visualise.new
  return visualise.validate_argv_length(argv) ||
    visualise.validate_probe_options(options) ||
    visualise.validate_assembly_options(options)
end

#write_orfs_to_file(found_orfs, orfs_file, translate = false) ⇒ Object 



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# File 'lib/finishm/orfs_finder.rb', line 108

def write_orfs_to_file(found_orfs, orfs_file, translate=false)
  if translate
      translator = Bio::AssemblyGraphAlgorithms::AllOrfsFinder.new
  end
  File.open(orfs_file,'w') do |f|
    counter = 0
    found_orfs.each do |name_and_sequence|
      counter += 1
      f.puts ">finishm_orf_#{counter} #{name_and_sequence[0]}"
      if translate
        f.puts translator.sequence2AA(name_and_sequence[1][0...-3])
      else
        f.puts name_and_sequence[1]
      end
    end
  end
end