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 15

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

#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_reference_coverage(crbblast) ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 28

def calculate_reference_coverage crbblast
  # The reciprocals hash in crb blast has contig names as the key.
  # In order to look up by the reference name we need to reverse this.
  # Scan through the reciprocals and get this Hit objects and add them to
  #   the @reference object for each reference sequence
  get_reference_hits crbblast
  per_query_contig_reference_coverage
  per_target_contig_reference_coverage crbblast
end

#get_reference_hits(crbblast) ⇒ Object 



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

def get_reference_hits crbblast
  @reference.each do |name, contig|
    contig.hits = []
  end
  crbblast.reciprocals.each do |query_id, list|
    list.each do |hit|
      unless @reference.assembly.key? hit.target
        raise TransrateError.new "#{hit.target} not in reference"
      end
      @reference[hit.target].hits << hit
    end
  end
  @comp_stats[:CRBB_hits] = crbblast.size
  @comp_stats[:n_contigs_with_CRBB] = crbblast.reciprocals.size
  @comp_stats[:p_contigs_with_CRBB] = crbblast.reciprocals.size/@assembly.size.to_f
end

#per_query_contig_reference_coverage ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 55

def per_query_contig_reference_coverage
  # for each query contig in the @assembly find out how much it covers
  # the reference
  n_refs_with_recip = 0
  total_crbb_hits = 0
  @reference.each do |ref_contig_name, ref_contig|
    ref_contig.hits.each do |hit| # a Hit from query to target
      query_contig_name = hit.query
      unless @assembly.assembly.key? query_contig_name
        raise TransrateError.new "#{query_contig_name} not in assembly"
      end
      @assembly[query_contig_name].has_crb = true
      @assembly[query_contig_name].hits << hit
      raise TransrateError.new "query should not be protein" if hit.qprot
      if hit.tprot
        coverage = 3*hit.alnlen+2 - 3*hit.mismatches - 3*hit.gaps
        coverage /= 3.0*hit.tlen
      else
        coverage = hit.alnlen - hit.mismatches - hit.gaps
        coverage /= hit.tlen.to_f
      end
      @assembly[query_contig_name].reference_coverage = coverage
    end

    if ref_contig.hits.size > 0 # this reference has a crbblast hit
      n_refs_with_recip += 1
    end
    total_crbb_hits += ref_contig.hits.size
  end
  @comp_stats[:rbh_per_reference] = total_crbb_hits / @reference.size.to_f
  @comp_stats[:n_refs_with_CRBB] = n_refs_with_recip
  @comp_stats[:p_refs_with_CRBB] = n_refs_with_recip / @reference.size.to_f
end

#per_target_contig_reference_coverage(crbblast) ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 89

def per_target_contig_reference_coverage crbblast
  # each target sequence in the reference can have multiple query contigs
  # hit it. to calculate the reference coverage you can't just add up the
  # alignment lengths. you have to make sure that overlaps are taken into
  # account
  coverage_thresholds = [0.25, 0.5, 0.75, 0.85, 0.95]
  coverage_totals = [0, 0, 0, 0, 0]
  prot = crbblast.target_is_prot
  total_coverage = 0
  total_length = 0
  @reference.each do |ref_contig_name, ref_contig|
    if prot
      covered = Array.new(ref_contig.length*3, false)
    else
      covered = Array.new(ref_contig.length, false)
    end
    ref_contig.hits.each_with_index do |hit, i| # a Hit from query to target
      if prot
        if hit.qstart % 3 == 0
          tstart = 3*hit.tstart-4
          tend = 3*hit.tend
        elsif hit.qstart % 3 == 1
          tstart = 3*hit.tstart-2
          tend = 3*hit.tend
        elsif hit.qstart % 3 == 2
          tstart = 3*hit.tstart-3
          tend = 3*hit.tend-1
        end
        if hit.qlen % 3 == 1
          tend += 1
        elsif hit.qlen % 3 == 2
          tend += 2
        end
      else
        tstart = hit.tstart
        tend = hit.tend
      end
      (tstart..tend).each do |b|
        covered[b-1] = true # blast coords are 1 indexed
      end
    end
    coverage = covered.reduce(0) { |sum, v| v ? sum + 1 : sum }
    ref_p = coverage / covered.length.to_f
    ref_contig.reference_coverage = ref_p
    coverage_thresholds.each_with_index do |n, index|
      if ref_p >= n
        coverage_totals[index] += 1
      end
    end

    total_coverage += coverage
    total_length += covered.length
  end

  # calculate proportion of ref sequences with coveragre over thresholds
  coverage_thresholds.each_with_index do |p, i|
    @comp_stats["cov#{(100*p).to_i}".to_sym] = coverage_totals[i]
    @comp_stats["p_cov#{(100*p).to_i}".to_sym] =
                                    coverage_totals[i]/@reference.size.to_f
  end
  @comp_stats[:reference_coverage] = total_coverage / total_length.to_f
end

#run ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 22

def run
  crbblast = run_crb_blast
  calculate_reference_coverage crbblast
  @has_run = true
end

#run_crb_blast ⇒ Object 



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# File 'lib/transrate/comparative_metrics.rb', line 152

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