Contents

#!/usr/bin/env ruby
require "bio"
require "thor"


class AcnfpTransCounter < Thor
  desc "analyse FILENAME", "Run acnfp-trans-counter on a given alignment"
  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
end


AcnfpTransCounter.start

Version data entries

1 entries across 1 versions & 1 rubygems

Version	Path
acnfp-trans-counter-0.2.0	bin/acnfp-trans-counter