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
10,0000.110.09?801  40% 89% 10% 20%
10,0000.100.07?801  86% 17% 29% 14%
10,0000.090.07?801  17% 17% 71% 17%

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 #2 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 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

Tue, 09 Jul 2019 18:38:24 GMT

COMMAND LINE:
/usr/bin/python3.9 knucleotide.python-dev-2.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

Revised BSD license

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