performance measurements

Each table row shows performance measurements for this PyPy program with a particular command-line input value N.

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
10,0000.510.6979,036777  100% 100% 100% 100%
10,0000.500.8274,856777  100% 100% 100% 100%
10,0000.500.6075,236777  100% 100% 100% 100%

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 PyPy #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

Wed, 16 Oct 2019 06:55:02 GMT

COMMAND LINE:
/usr/bin/pypy knucleotide.pypy-8.pypy 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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