performance measurements
Each table row shows performance measurements for this program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|
Read the ↓ make, command line, and program output logs to see how this program was run.
Read benchmark to see what this program should do.
notes
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 jacek2v: few changes in algorytm, added multiprocessing, used str.count (nucleo newer overlapping)
from sys import stdin
from collections import defaultdict
from multiprocessing import Process, Pool, cpu_count
def gen_freq(seq, frame):
frequences = defaultdict(int)
ns = len(seq) + 1 - frame
for ii in range(ns):
frequences[seq[ii:ii + frame]] += 1
return ns, frequences
def sort_seq(seq, length):
n, frequences = gen_freq(seq, length)
#l = sorted(frequences.items(), reverse=True, key=lambda (seq,freq): (freq,seq))
l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1],seq_freq[0]))
return [(st, 100.0*fr/n) for st, fr in l]
def find_seq(seq, nucleo):
count = seq.count(nucleo)
return nucleo, count
def load():
for line in stdin:
if line[0:3] == ">TH":
break
seq = []
for line in stdin:
if line[0] in ">;":
break
seq.append( line[:-1] )
return seq
def main():
nucleos = "GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT"
sequence = "".join(load()).upper()
plres = []
pl = Pool(processes=cpu_count() + 1)
for nl in 1,2:
plres.append(pl.apply_async(sort_seq, (sequence, nl, )))
for se in nucleos.split():
plres.append(pl.apply_async(find_seq, (sequence, se, )))
pl.close()
pl.join()
for ii in 0,1:
print('\n'.join("%s %.3f" % (st, fr) for st,fr in plres[ii].get()))
print('')
for ii in range(2, len(nucleos.split()) + 2):
print("%d\t%s" % (plres[ii].get()[1], plres[ii].get()[0]))
main()
make, command-line, and program output logs
Sun, 23 Apr 2023 09:14:44 GMT MAKE: make[1]: Vstupuje se do adresáře „/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp“ cp knucleotide.cython-2.cython `echo knucleotide.cython-2.cython | sed 's/cython-..//' | sed 's/.cython//'`.pyx cythonize -3 -bi `echo knucleotide.cython-2.cython | sed 's/cython-..//' | sed 's/.cython//'`.pyx Compiling /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.pyx because it changed. [1/1] Cythonizing /home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp/knucleotide.pyx make[1]: Opouští se adresář „/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp“ 3.92s to complete and log all make actions COMMAND LINE: /usr/bin/python3 -c "import knucleotide" 0 < knucleotide-input10000.txt TIMED OUT after 300s PROGRAM OUTPUT: