Class: Transrate::ComparativeMetrics

Inherits:
Object
  • Object
show all
Defined in:
lib/transrate/comparative_metrics.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(assembly, reference, threads) ⇒ ComparativeMetrics

Returns a new instance of ComparativeMetrics.



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# File 'lib/transrate/comparative_metrics.rb', line 16

def initialize assembly, reference, threads
  @assembly = assembly
  @reference = reference
  @threads = threads
  @comp_stats = Hash.new
end

Instance Attribute Details

#comp_stats ⇒ Object (readonly)

Returns the value of attribute comp_stats.



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# File 'lib/transrate/comparative_metrics.rb', line 13

def comp_stats
  @comp_stats
end

#has_run ⇒ Object (readonly)

Returns the value of attribute has_run.



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# File 'lib/transrate/comparative_metrics.rb', line 11

def has_run
  @has_run
end

#n_chimeras ⇒ Object (readonly)

Returns the value of attribute n_chimeras.



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# File 'lib/transrate/comparative_metrics.rb', line 14

def n_chimeras
  @n_chimeras
end

#p_chimeras ⇒ Object (readonly)

Returns the value of attribute p_chimeras.



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# File 'lib/transrate/comparative_metrics.rb', line 14

def p_chimeras
  @p_chimeras
end

#rbh_per_contig ⇒ Object (readonly)

Returns the value of attribute rbh_per_contig.



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# File 'lib/transrate/comparative_metrics.rb', line 8

def rbh_per_contig
  @rbh_per_contig
end

#rbh_per_reference ⇒ Object (readonly)

Returns the value of attribute rbh_per_reference.



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# File 'lib/transrate/comparative_metrics.rb', line 9

def rbh_per_reference
  @rbh_per_reference
end

#reciprocal_hits ⇒ Object (readonly)

Returns the value of attribute reciprocal_hits.



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# File 'lib/transrate/comparative_metrics.rb', line 10

def reciprocal_hits
  @reciprocal_hits
end

#reference_coverage ⇒ Object (readonly)

Returns the value of attribute reference_coverage.



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# File 'lib/transrate/comparative_metrics.rb', line 12

def reference_coverage
  @reference_coverage
end

Instance Method Details

#calculate_coverage(blocks) ⇒ Object

Calculate the total coverage from a set of coverage blocks



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# File 'lib/transrate/comparative_metrics.rb', line 191

def calculate_coverage blocks
  coverage = 0
  blocks.each do |block|
    if block[0] and block[1]
      if block[0]>=0 and block[1]>=0
        coverage += block[1] - block[0] + 1
      end
    else
      puts "error: key = #{key}, #{blocks}"
    end
  end
  coverage
end

#chimeras(crbblast) ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 213

def chimeras crbblast
  @n_chimeras = 0
  crbblast.reciprocals.each_pair do |key, list|
    p = 0
    list.each_with_index do |a, i|
      list.each_with_index do |b, j|
        if j>i
          if a.target == b.target
            astart, astop = [a.tstart, a.tend].minmax
            bstart, bstop = [b.tstart, b.tend].minmax

            oa = overlap_amount(astart, astop, bstart, bstop)
            if oa > 0.75
              p += 1
            end
          else
            astart, astop = [a.qstart, a.qend].minmax
            bstart, bstop = [b.qstart, b.qend].minmax

            oa = overlap_amount(astart, astop, bstart, bstop)
            if oa < 0.25
              p += 1
            end
          end
        end
      end
    end
    if p/list.size.to_f >= 0.5
      @n_chimeras += 1
      unless @assembly.assembly.key? key
        puts "key not in assembly: #{key}"
      end
      @assembly[key].is_chimera = true
    end
  end
  @p_chimeras = @n_chimeras / crbblast.reciprocals.length.to_f
end

#collapse_factor(reciprocals) ⇒ Object

Count unique reference proteins per contig



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# File 'lib/transrate/comparative_metrics.rb', line 304

def collapse_factor reciprocals
  return @collapse_factor unless @collapse_factor.nil?
  cf_sum = 0
  reciprocals.each do |query, hits|
    uniq_hits = Set.new hits.map{ |h| h.target }
    cf = uniq_hits.length
    @assembly[query].collapse_factor = cf
    cf_sum += cf
  end
  cf_sum / reciprocals.size
end

#count_ref_crbbs ⇒ Object

Count reference proteins with at least one recprocal hit



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# File 'lib/transrate/comparative_metrics.rb', line 206

def count_ref_crbbs
  @n_refs_with_recip = @reference.assembly.inject(0) do |sum, entry|
    name, contig = entry
    sum + (contig.hits.length > 0 ? 1 : 0)
  end
end

#coverage(crbblast) ⇒ Object

coverage of contigs that have reciprocal hits divided by number of reciprocal targets



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# File 'lib/transrate/comparative_metrics.rb', line 59

def coverage crbblast
  return @reference_coverage unless @reference_coverage.nil?
  crbblast.reciprocals.each do |key, list|
    list.each_with_index do |hit, i|
      unless @reference.assembly.key? hit.target
        raise "#{hit.target} not in reference"
      end
      @reference[hit.target].hits << hit

      unless @assembly.assembly.key? hit.query
        raise "#{hit.query} not in assembly"
      end
      contig = @assembly[hit.query]
      contig.has_crb = true
      # how much of the reference is covered by this single contig
      contig.reference_coverage = hit.alnlen / hit.tlen
      contig.hits << hit
    end
  end
  total_coverage = 0
  total_length = 0
  cov = [0.25, 0.5, 0.75, 0.85, 0.95]
  @reference.each_value do |ref_contig|
    key = ref_contig.name
    list = ref_contig.hits
    total_length += crbblast.target_is_prot ? ref_contig.length : ref_contig.length*3

    next if list.empty? # ah this is what was breaking everything
    blocks = []
    target_length = 0
    list.each do |hit|
      target_length = hit.tlen
      if crbblast.target_is_prot
        target_length *= 3
        start, stop = [hit.tstart, hit.tend].minmax
        start = start*3-2
        stop = stop*3
      else
        start, stop = [hit.tstart, hit.tend].minmax
      end
      if blocks.empty?
        blocks << [start, stop]
      else
        found=false
        blocks.each do |block|
          # if query overlaps with any block extend that block
          o = overlap(block[0], block[1], start, stop)
          if o == 0 # perfect overlap
            found=true
          elsif o == 1 # partial overlap
            block[0] = start
            found=true
          elsif o == 2 # partial overlap
            block[1] = stop
            found=true
          elsif o == 3 # full overlap
            block[0] = start
            block[1] = stop
            found=true
          elsif o == 4 # full overlap
            found=true
            # nothing
          # elsif o == 5 || o == 6 # no overlap

          end
        end
        if !found
          blocks << [start, stop]
        end
        # if any blocks now overlap then extend one block and remove
        # the other
      end
    end
    blocks.each_with_index do |block_a,a|
      blocks.each_with_index do |block_b,b|
        if a!=b
          o = overlap(block_a[0], block_a[1], block_b[0], block_b[1])
          if o == 0 # perfect overlap
            block_b[0]=-1
            block_b[1]=-1
          elsif o == 1 # partial overlap
            block_a[0] = block_b[0]
            block_b[0] = -1
            block_b[1] = -1
          elsif o == 2 # partial overlap
            block_a[1] = block_b[1]
            block_b[0] = -1
            block_b[1] = -1
          elsif o == 3 # full overlap
            block_a[0] = block_b[0]
            block_a[1] = block_b[1]
            block_b[0] = -1
            block_b[1] = -1
          elsif o == 4 # full overlap
            block_b[0] = -1
            block_b[1] = -1
          # elsif o == 5 || o == 6# no overlap
            # do nothing
          # elsif  # no overlap
            # do nothing
          end
        end
      end # each_with_index b
    end # each_with_index a
    # sum blocks to find total coverage
    length_of_coverage = calculate_coverage blocks
    @cov ||= [0, 0, 0, 0, 0]
    if target_length > 0
      # puts "#{length_of_coverage} / #{target_length.to_f}"
      ref_p = length_of_coverage / target_length.to_f
    else
      ref_p = 0
    end
    ref_contig.reference_coverage = ref_p

    cov.each_with_index do |c, i|
      if ref_p >= c
        @cov[i] +=1
      end
    end

    total_coverage += length_of_coverage
  end
  cov.each_with_index do |p, i|
    @comp_stats["cov#{(100*p).to_i}".to_sym] = @cov[i]
    @comp_stats["p_cov#{(100*p).to_i}".to_sym] =
                                              @cov[i]/@reference.size.to_f
  end
  total_coverage / total_length.to_f
end

#overlap(astart, astop, bstart, bstop) ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 251

def overlap(astart, astop, bstart, bstop)
  if astart == bstart and astop == bstop
    return 0
  elsif astart < bstart
    if astop > bstart
      if astop > bstop
        return 4
      else
        return 2
      end
    else
      return 5 # no overlap
    end
  else
    if bstop > astart
      if bstop > astop
        return 3
      else
        return 1
      end
    else
      return 6 # no overlap
    end
  end
end

#overlap_amount(astart, astop, bstart, bstop) ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 277

def overlap_amount(astart, astop, bstart, bstop)
  if astart == bstart and astop == bstop
    return 1
  elsif astart < bstart
    if astop > bstart
      if astop > bstop
        return (bstop-bstart+1)/(astop-astart+1).to_f # 4
      else
        return (astop-bstart+1)/(bstop-astart+1).to_f # 2
      end
    else
      return 0 # 5 no overlap
    end
  else
    if bstop > astart
      if bstop > astop
        return (astop-astart+1)/(bstop-bstart+1).to_f # 3
      else
        return (bstop-astart+1)/(astop-bstart+1).to_f # 1
      end
    else
      return 0 # 6 no overlap
    end
  end
end

#reciprocal_best_blast ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 51

def reciprocal_best_blast
  crbblast = CRB_Blast::CRB_Blast.new @assembly.file, @reference.file
  crbblast.run(1e-5, @threads, true)
  crbblast
end

#run ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 23

def run
  @crbblast = reciprocal_best_blast
  @reference_coverage = coverage @crbblast
  @collapse_factor = collapse_factor @crbblast.reciprocals
  @reciprocal_hits = @crbblast.size
  @rbh_per_reference = @reciprocal_hits.to_f / @reference.size.to_f
  @p_contigs_with_recip = @crbblast.reciprocals.size / @assembly.size.to_f
  @n_contigs_with_recip = @crbblast.reciprocals.size
  count_ref_crbbs
  @p_refs_with_recip = @n_refs_with_recip / @reference.size.to_f
  chimeras @crbblast
  self.run_comp_stats
  @has_run = true
end

#run_comp_stats ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 38

def run_comp_stats
  @comp_stats[:CRBB_hits] = @reciprocal_hits # CRBB hits
  @comp_stats[:p_contigs_with_CRBB] = @p_contigs_with_recip
  @comp_stats[:n_contigs_with_CRBB] = @n_contigs_with_recip
  @comp_stats[:p_refs_with_CRBB] = @p_refs_with_recip
  @comp_stats[:n_refs_with_CRBB] = @n_refs_with_recip
  @comp_stats[:rbh_per_reference] = @rbh_per_reference
  @comp_stats[:reference_coverage] = @reference_coverage
  @comp_stats[:collapse_factor] = @collapse_factor
  @comp_stats[:n_chimeras] = @n_chimeras
  @comp_stats[:p_chimeras] = @p_chimeras
end