Class: Bio::BFRTools::BFRContainer

Inherits:

Container

• Object
• Container
• Bio::BFRTools::BFRContainer

Defined in:

lib/bio/BFRTools.rb

Constant Summary

Constants inherited from Container

Container::BASES

Instance Attribute Summary

Attributes inherited from Container

#bulk_1_name, #bulk_1_sam, #bulk_2_name, #bulk_2_sam, #parental_1_name, #parental_1_sam, #parental_2_name, #parental_2_sam, #processed_regions, #putative_snps, #reference_db, #total_length

Instance Method Summary

• #get_region(opts = {}) ⇒ Object
• #init_counters ⇒ Object
• #print_header(opts = {}) ⇒ Object
• #print_stats(opts = {}) ⇒ Object
• #process_region(opts = {}) ⇒ Object

Methods inherited from Container

#bulk_1, #bulk_2, #parental_1, #parental_2, #reference, #reference_sequence, snps_between

Instance Method Details

#get_region(opts = {}) ⇒ Object

# File 'lib/bio/BFRTools.rb', line 386

def get_region(opts={})
  opts[:container] = self
  region = BFRRegion.new(opts)
end

#init_counters ⇒ Object

# File 'lib/bio/BFRTools.rb', line 362

def init_counters
  @putative_snps      = 0
  @proccesed_regions  = 0
  @not_enogh_coverage = 0
  @total_avg_coverage_bulk_1 = 0.0
  @total_avg_coverage_bulk_2 = 0.0
  @total_snp_1kbp = 0.0
  @no_snps = 0
  @too_many_snps = 0

end

#print_header(opts = {}) ⇒ Object

# File 'lib/bio/BFRTools.rb', line 373

def print_header(opts={}) 
  output = opts[:output_file_stats] ? opts[:output_file_stats] : $stderr
  output.print "#bulk_1\tbulk_2\tProcessed_regions\tputative_snps\tno_snps\ttoo_many_snps\tno_enough_coverage\tavg_cov_bulk_1\tavg_cov_bulk_2\tavg_snp_1kbp\n"
end

#print_stats(opts = {}) ⇒ Object

# File 'lib/bio/BFRTools.rb', line 378

def print_stats(opts={}) 
  output = opts[:output_file_stats] ? opts[:output_file_stats] : $stderr
  output.print @bulk_1_name, "\t", @bulk_2_name, "\t"
  output.print @proccesed_regions, "\t", @putative_snps, "\t", @no_snps, "\t", @too_many_snps,"\t", @not_enogh_coverage, "\t"
  output.print @total_avg_coverage_bulk_1/@proccesed_regions, "\t",@total_avg_coverage_bulk_2/@proccesed_regions, "\t" 
  output.print @total_snp_1kbp / @proccesed_regions,"\n"
end

#process_region(opts = {}) ⇒ Object

# File 'lib/bio/BFRTools.rb', line 391

def process_region(opts={})        
  opts = { :min_cov=>20, :max_snp_1kbp => 10, :max_per=>0.20 }.merge!(opts)

  @proccesed_regions += 1
  output = opts[:output_file] ? opts[:output_file] : $stdout
  print_output = opts[:output_file] ? true : false
  opts[:container] = self

  region = BFRRegion.new(opts)

  #puts region.to_multi_fasta

  @total_snp_1kbp += region.snp_1kbp 
 # puts "SNPS: #{region.snp_1kbp}"
  if region.snp_count == 0
    @no_snps += 1 
    print_output = false 
  end

  if region.snp_1kbp  > opts[:max_snp_1kbp]
    @too_many_snps += 1
    print_output = false
  end



  @total_avg_coverage_bulk_2 += region.avg_cov_bulk_2
  @total_avg_coverage_bulk_1 += region.avg_cov_bulk_1

  if region.avg_cov_bulk_2 < opts[:min_cov] or region.avg_cov_bulk_1 < opts[:min_cov]
    @not_enogh_coverage += 1
    print_output = false
  end

  info = Array.new

  if print_output
    for i in (0..region.size-1)
      if region.coverages_1[i] > opts[:min_cov] and region.coverages_2[i] > opts[:min_cov]
        BASES.each do |base|

          info.clear
          if  Bio::NucleicAcid.is_valid( region.parental_1_sequence[i],  base.to_s  ) and 
            not  Bio::NucleicAcid.is_valid( region.parental_2_sequence[i],  base.to_s  )
            info << :first
          end

          if   Bio::NucleicAcid.is_valid( region.parental_2_sequence[i],  base.to_s  ) and 
            not Bio::NucleicAcid.is_valid( region.parental_1_sequence[i],  base.to_s  )
            info << :second
          end


          for informative in info
            line = region.get_bfr_line(i, base, informative)
            output.print  line , "\n"
          end
        end
      end
    end
  end


  @parental_1_sam.mpileup_clear_cache region
  @parental_2_sam.mpileup_clear_cache region
  @bulk_2_sam.mpileup_clear_cache region
  @bulk_1_sam.mpileup_clear_cache region
  return region
end