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|
prelude: |
bm_so_fasta = <<'EOS'
# The Computer Language Shootout
# http://shootout.alioth.debian.org/
# Contributed by Sokolov Yura
$last = 42.0
def gen_random(max, im=139968, ia=3877, ic=29573)
(max * ($last = ($last * ia + ic) % im)) / im
end
alu =
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"+
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"+
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"+
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"+
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"+
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"+
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
iub = [
["a", 0.27],
["c", 0.12],
["g", 0.12],
["t", 0.27],
["B", 0.02],
["D", 0.02],
["H", 0.02],
["K", 0.02],
["M", 0.02],
["N", 0.02],
["R", 0.02],
["S", 0.02],
["V", 0.02],
["W", 0.02],
["Y", 0.02],
]
homosapiens = [
["a", 0.3029549426680],
["c", 0.1979883004921],
["g", 0.1975473066391],
["t", 0.3015094502008],
]
def make_repeat_fasta(id, desc, src, n)
puts ">#{id} #{desc}"
v = nil
width = 60
l = src.length
s = src * ((n / l) + 1)
s.slice!(n, l)
puts(s.scan(/.{1,#{width}}/).join("\n"))
end
def make_random_fasta(id, desc, table, n)
puts ">#{id} #{desc}"
rand, v = nil,nil
width = 60
chunk = 1 * width
prob = 0.0
table.each{|v| v[1]= (prob += v[1])}
for i in 1..(n/width)
puts((1..width).collect{
rand = gen_random(1.0)
table.find{|v| v[1]>rand}[0]
}.join)
end
if n%width != 0
puts((1..(n%width)).collect{
rand = gen_random(1.0)
table.find{|v| v[1]>rand}[0]
}.join)
end
end
n = (ARGV[0] or 250_000).to_i
make_repeat_fasta('ONE', 'Homo sapiens alu', alu, n*2)
make_random_fasta('TWO', 'IUB ambiguity codes', iub, n*3)
make_random_fasta('THREE', 'Homo sapiens frequency', homosapiens, n*5)
EOS
benchmark:
- name: so_k_nucleotide
prelude: |
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
File.write(script, bm_so_fasta)
def prepare_fasta_output n
filebase = File.join(File.dirname($0), 'fasta.output')
script = File.join(File.dirname($0), 'bm_so_fasta.rb')
file = "#{filebase}.#{n}"
unless FileTest.exist?(file)
STDERR.puts "preparing #{file}"
open(file, 'w'){|f|
ARGV[0] = n
$stdout = f
load script
$stdout = STDOUT
}
end
end
prepare_fasta_output(100_000)
script: |
# 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) }
loop_count: 1
|
