Class: Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter

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

Instance Method Summary collapse

Methods included from FinishM::Logging

#log

Instance Method Details

#filter(paths, kmer_hash, thresholds, options = {}) ⇒ Object

Remove all paths where the kmer coverage is below the threshold at any point along the path.

:paths: an iterable collection of paths :kmer_hash: KmerMultipleAbundanceHash :thresholds: minimum coverages (min numbers of full kmers) required at each point along the path

Optional options

  • :exclude_ending_length => don’t filter out paths based on kmers close to the end e.g. :exclude_ending_length => 2 means the first 2 and last 2 kmers are not considered



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# File 'lib/assembly/kmer_coverage_based_path_filter.rb', line 16

def filter(paths, kmer_hash, thresholds, options={})
  # sanity check
  unless kmer_hash.number_of_abundances == thresholds.length
    raise "Unexpectedly found a different number of thresholds and kmer abundance columns"
  end

  passable_paths = []
  paths.each do |path|
    passable = true
    seq = path.sequence

    # remove ends of sequence if kmers don't count at the ends
    if options[:exclude_ending_length]
      ex = options[:exclude_ending_length]
      seq = seq[ex...(seq.length-ex)]
    end

    Bio::Sequence::NA.new(seq).window_search(kmer_hash.kmer_length,1) do |kmer|
      kmer_hash[kmer].each_with_index do |abundance, i|
        if abundance < thresholds[i]
          passable = false
          log.debug "Failing trail #{path.sequence} due to insufficent abundance (#{abundance} from #{kmer_hash[kmer]}) for #{kmer}" if log.debug?
          break
        end
      end
      break if !passable
    end
    passable_paths.push path if passable
  end
  return passable_paths
end

#write_depths(io, trail_name, trail_sequence, kmer_hash) ⇒ Object

Write coverages to the given IO object as a tab-separated file similar to the output of “samtools depth”



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# File 'lib/assembly/kmer_coverage_based_path_filter.rb', line 50

def write_depths(io, trail_name, trail_sequence, kmer_hash)
  #write header
  io.print %w(trail position).join("\t")
  io.print "\t"
  kmer_hash.number_of_abundances.times{|i| io.print "\tcoverage#{i+1}"}
  io.puts

  #write data
  pos = 1
  Bio::Sequence::NA.new(trail_sequence).window_search(kmer_hash.kmer_length,1) do |kmer|
    io.puts [trail_name, pos, kmer_hash[kmer]].flatten.join("\t")
    pos += 1
  end
end