Class: Bio::AssemblyGraphAlgorithms::PairedEndAssembler

Inherits:
SingleEndedAssembler show all
Includes:
FinishM::Logging
Defined in:
lib/assembly/paired_end_assembler.rb

Constant Summary

Constants inherited from SingleEndedAssembler

SingleEndedAssembler::ASSEMBLY_OPTIONS, SingleEndedAssembler::DEFAULT_MAX_TIP_LENGTH, SingleEndedAssembler::DEFAULT_MIN_CONFIRMING_RECOHERENCE_READS, SingleEndedAssembler::DEFAULT_MIN_CONTIG_SIZE

Instance Attribute Summary

Attributes inherited from SingleEndedAssembler

#assembly_options, #graph

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Methods inherited from SingleEndedAssembler

#assemble, #find_beginning_trail_from_node, #find_tip_distance, #gather_starting_nodes, #initialize, #is_short_tip?, #remove_seen_nodes_from_end_of_path, #remove_tips, #seen_last_in_path?, #setup_progressbar

Constructor Details

This class inherits a constructor from Bio::AssemblyGraphAlgorithms::SingleEndedAssembler

Instance Method Details

#assemble_from(initial_path, visited_nodes) ⇒ Object

Assemble considering reads as a possibly paired-ended. Options are as per SingleEndedAssembler#assemble_from, with the addition of :min_insert_size: minimum length of fragment pair required to satisfy the additional constraints of the paired end assembler. :max_insert_size: maximum length of fragment pair.



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# File 'lib/assembly/paired_end_assembler.rb', line 9

def assemble_from(initial_path, visited_nodes)
  visited_nodes = Set.new
  while true
    # Try to assemble using single ended techniques first, and only if that fails fall
    # back to paired-end techniques.
    path, visited_nodes, next_neighbours = super(initial_path, visited_nodes)

    # The next_neighbours
    if next_neighbours.empty?
      # No-where to go, do nothing
      # TODO: try to jump over the gap using paired-end sequences
    elsif next_neighbours.length < 2
      raise "Programming error"
    else
      # Choose between forks based on paired-end data
      next_neighbours.select! do |oneigh|
        confirm_connection_backwards(oneigh, path)
      end
    end
  end
end

#confirm_connection_backwards(new_onode, current_path, min_insert_size, max_insert_size) ⇒ Object

Return true if the backward connection is strong enough to warrant adding the new_node to the current_path. Else return false

In order to qualify as a warranted path, reads from the pair must have at least 1 connection backwards at least options backwards from the end of the current path, but not more than options Connection length is the length of the read pair’s insert size.



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# File 'lib/assembly/paired_end_assembler.rb', line 38

def confirm_connection_backwards(new_onode, current_path, min_insert_size, max_insert_size)
  min_insert_size = @assembly_options[:min_insert_size]
  max_insert_size = @assembly_options[:max_insert_size]

  # Collect the reads that would qualify if they were in the new node
  qualifying_reads = Set.new
  current_path.reverse.each do |node|

  end

  # Look at all the sequences in the new onode. Do any of them qualify
  new_onode.node.short_reads.each do |short|

  end
end