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