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# The Computer Language Shootout
# http://shootout.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
input = open(File.join(File.dirname($0), 'fasta.output.100000'), 'rb')
line = input.gets while line !~ /^>THREE/
line = input.gets
while (line !~ /^>/) & line do
seq << line.chomp
line = input.gets
end
[1,2].each {|i| sort_by_freq( seq,i ) }
%w(ggt ggta ggtatt ggtattttaatt ggtattttaatttatagt).each{|s| find_seq( seq,s) }
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