1# The Computer Language Shootout 2# http://shootout.alioth.debian.org 3# 4# contributed by jose fco. gonzalez 5# modified by Sokolov Yura 6 7seq = String.new 8 9def frecuency( seq,length ) 10 n, table = seq.length - length + 1, Hash.new(0) 11 f, i = nil, nil 12 (0 ... length).each do |f| 13 (f ... n).step(length) do |i| 14 table[seq[i,length]] += 1 15 end 16 end 17 [n,table] 18 19end 20 21def sort_by_freq( seq,length ) 22 n,table = frecuency( seq,length ) 23 a, b, v = nil, nil, nil 24 table.sort{|a,b| b[1] <=> a[1]}.each do |v| 25 puts "%s %.3f" % [v[0].upcase,((v[1]*100).to_f/n)] 26 end 27 puts 28end 29 30def find_seq( seq,s ) 31 n,table = frecuency( seq,s.length ) 32 puts "#{table[s].to_s}\t#{s.upcase}" 33end 34 35input = open(File.join(File.dirname($0), 'fasta.output.100000'), 'rb') 36 37line = input.gets while line !~ /^>THREE/ 38line = input.gets 39 40while (line !~ /^>/) & line do 41 seq << line.chomp 42 line = input.gets 43end 44 45[1,2].each {|i| sort_by_freq( seq,i ) } 46 47%w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt).each{|s| find_seq( seq,s) } 48 49