performance measurements
Each table row shows performance measurements for this Python dev program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 10,000 | 0.12 | 0.06 | ? | 777 | 67% 20% 20% 17% 29% 33% 20% 43% |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read k-nucleotide benchmark to see what this program should do.
notes
k-nucleotide Python dev #8 program source code
# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# modified by xfm for parallelization
# modified by Justin Peel
from sys import stdin
from collections import defaultdict
from multiprocessing import Pool
def gen_freq(frame) :
global sequence
frequences = defaultdict(int)
if frame != 1:
for ii in range(len(sequence)-frame+1) :
frequences[sequence[ii:ii+frame]] += 1
else:
for nucleo in sequence:
frequences[nucleo] += 1
return frequences
def sort_seq(length):
frequences = gen_freq(length)
n= sum(frequences.values())
l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1],seq_freq[0]))
return '\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l)
def find_seq(s):
t = gen_freq(len(s))
return (s,t.get(s,0))
def prepare(f=stdin) :
for line in f:
if line[0] in ">;":
if line[1:3] == "TH":
break
seq = []
app = seq.append
for line in f:
if line[0] in ">;":
break
app( line )
return "".join(seq).upper().replace('\n','')
def init(arg):
global sequence
sequence = arg
def main():
global sequence
sequence = prepare()
p=Pool()
res2 = p.map_async(find_seq,reversed("GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT".split()))
res1 = p.map_async(sort_seq,(1,2))
for s in res1.get() : print (s+'\n')
res2 = reversed([r for r in res2.get()])
print ("\n".join("{1:d}\t{0}".format(*s) for s in res2))
if __name__=='__main__' :
main()
make, command-line, and program output logs
Fri, 09 Sep 2022 06:02:57 GMT COMMAND LINE: /usr/bin/python3.12 knucleotide.python-dev-8.python-dev 0 < knucleotide-input10000.txt PROGRAM OUTPUT: A 30.284 T 29.796 C 20.312 G 19.608 AA 9.212 AT 8.950 TT 8.948 TA 8.936 CA 6.166 CT 6.100 AC 6.086 TC 6.042 AG 6.036 GA 5.968 TG 5.868 GT 5.798 CC 4.140 GC 4.044 CG 3.906 GG 3.798 562 GGT 152 GGTA 15 GGTATT 0 GGTATTTTAATT 0 GGTATTTTAATTTATAGT