The Computer Language
Benchmarks Game

k-nucleotide Ruby #2 program

source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org
#
# contributed by jose fco. gonzalez
# modified by Sokolov Yura

seq = String.new

def frecuency( seq,length )
    n, table = seq.length - length + 1, Hash.new(0)
    f, i = nil, nil
    (0 ... length).each do |f|
        (f ... n).step(length) do |i|
            table[seq[i,length]] += 1
        end
    end
    [n,table]

end

def sort_by_freq( seq,length )
    n,table = frecuency( seq,length )
    a, b, v = nil, nil, nil
    table.sort{|a,b| b[1] <=> a[1]}.each do |v|
        puts "%s %.3f" % [v[0].upcase,((v[1]*100).to_f/n)]
    end
    puts
end

def find_seq( seq,s )
    n,table = frecuency( seq,s.length )
    puts "#{table[s].to_s}\t#{s.upcase}"
end

line = STDIN.gets while line !~ /^>THREE/
line = STDIN.gets
while (line !~ /^>/) & line do
    seq << line.chomp
    line = STDIN.gets
end

[1,2].each {|i| sort_by_freq( seq,i ) }

%w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt).each{|s| find_seq( seq,s) }
    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
ruby 2.4.0p0 (2016-12-24 revision 57164) [x86_64-linux]


Wed, 15 Feb 2017 02:19:27 GMT

COMMAND LINE:
/usr/local/src/ruby/bin/ruby -W0 knucleotide.yarv-2.yarv 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT