performance measurements

Each table row shows performance measurements for this Python 3 program with a particular command-line input value N.

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
10,0000.130.13?594  8% 21% 83% 8%
10,0000.120.12?594  8% 100% 0% 8%
10,0000.120.13?594  100% 8% 14% 8%

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

Python 3.3.1 (default, Apr 11 2013, 12:45:45)
[GCC 4.7.2] on linux

 k-nucleotide Python 3 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

Mon, 12 Nov 2018 12:07:44 GMT

COMMAND LINE:
/usr/bin/python3 knucleotide.python3 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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