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 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
250,0004.244.2431,240487  0% 0% 1% 100%
2,500,00042.6442.6764,580487  1% 0% 0% 100%
25,000,000427.56427.81402,016487  1% 0% 0% 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

Python 3.4.0 (default, Mar 17 2014, 08:05:26) [GCC 4.8.1] 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

Tue, 18 Mar 2014 10:01:10 GMT

MAKE:
mv knucleotide.python3 knucleotide.py
/usr/local/src/Python-3.4.0/bin/python3.4 -OO -c "from py_compile import compile; compile('knucleotide.py')"
0.24s to complete and log all make actions

COMMAND LINE:
/usr/local/src/Python-3.4.0/bin/python3.4 knucleotide.py 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT

Revised BSD license

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