Class: AcnfpTransCounter

Inherits:
Thor
  • Object
show all
Defined in:
bin/acnfp-trans-counter

Instance Method Summary collapse

Instance Method Details

#analyse(filename) ⇒ Object 



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# File 'bin/acnfp-trans-counter', line 8

def analyse(filename)
  alignments = Bio::FlatFile.open(filename)
  
  alignments.to_a.combination(2) do |a,b|
    transition_count = 0
    transversion_count = 0
    indel_count = 0
    informative_count = 0
    
    alignment = Bio::Alignment::OriginalAlignment.new([a,b])
    alignment.each_site do |site|
      next if site.has_gap?

      if site[0] == site[1] or site.include? "N"
        informative_count += 1
        next
      end
      
      case site.sort.map{|char| char.upcase}
      when %w{C T}, %w{A G}
        transition_count += 1
      when %w{A C}, %w{A T}, %w{C G}, %w{G T}
        transversion_count += 1
      else
        raise "Unknown pairing: #{site}"
      end
    end

    mutation_count = transversion_count + transition_count.to_f
    
    header = "%s vs %s" % [a.definition, b.definition]
    puts header
    puts "=" * header.length

    puts "Transversions: %d (%.2f%%)" % [transversion_count, 100 * transversion_count / mutation_count]
    puts "Transitions:   %d (%.2f%%)" % [transition_count, 100 * transition_count / mutation_count]
    puts "Transversions / Transitions: %.2f" % [transversion_count.to_f / transition_count]
    puts "Non-indel sites: %d" % informative_count
    puts
  end
end