performance measurements

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

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
10,0001.541.01320,944594  37% 22% 12% 89%
10,0001.551.01392,412594  41% 14% 28% 88%
10,0001.541.01390,844594  13% 49% 89% 15%

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 Graal program source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# 2to3

from sys import stdin

def gen_freq(seq, frame, frequences):
    ns = len(seq) + 1 - frame
    frequences.clear()
    for ii in range(ns):
        nucleo = seq[ii:ii + frame]
        if nucleo in frequences:
            frequences[nucleo] += 1
        else:
            frequences[nucleo] = 1
    return ns, frequences


def sort_seq(seq, length, frequences):
    n, frequences = gen_freq(seq, length, frequences)

    l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1],seq_freq[0]))

    print('\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l))
    print()


def find_seq(seq, s, frequences):
    n,t = gen_freq(seq, len(s), frequences)
    print("%d\t%s" % (t.get(s, 0), s))


def main():
    frequences = {}
    for line in stdin:
        if line[0:3] == ">TH":
            break

    seq = []
    for line in stdin:
        if line[0] in ">;":
            break
        seq.append( line[:-1] )
    sequence = "".join(seq).upper()

    for nl in 1,2:
        sort_seq(sequence, nl, frequences)

    for se in "GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT".split():
        find_seq(sequence, se, frequences)

main()

 make, command-line, and program output logs

Tue, 14 May 2019 09:23:36 GMT

COMMAND LINE:
/usr/bin/graalpython knucleotide.graal 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

Please note: This Python implementation is in the very early stages, and can run little more than basic benchmarks at this point.

Revised BSD license

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