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Computer Language Benchmarks Game      [[ Play ]]

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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
50,000	0.34	0.40	30,072	478	3% 0% 3% 88%
500,000	2.74	2.80	76,672	478	1% 0% 0% 98%
5,000,000	26.66	26.78	267,572	478	0% 0% 0% 100%

Read the ↓ make, command line, and program output logs to see how this program was run.

Read regex-dna 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

 regex-dna Python 3 program source code

# The Computer Language Benchmarks Game
# http://shootout.alioth.debian.org/
# contributed by Dominique Wahli
# 2to3
# mp by Ahmad Syukri
# modified by Justin Peel

from sys import stdin
from re import sub, findall
from multiprocessing import Pool

def init(arg):
    global seq
    seq = arg

def var_find(f):
    return len(findall(f, seq))

def main():
    seq = stdin.read()
    ilen = len(seq)

    seq = sub('>.*\n|\n', '', seq)
    clen = len(seq)

    pool = Pool(initializer = init, initargs = (seq,))

    variants = (
          'agggtaaa|tttaccct',
          '[cgt]gggtaaa|tttaccc[acg]',
          'a[act]ggtaaa|tttacc[agt]t',
          'ag[act]gtaaa|tttac[agt]ct',
          'agg[act]taaa|ttta[agt]cct',
          'aggg[acg]aaa|ttt[cgt]ccct',
          'agggt[cgt]aa|tt[acg]accct',
          'agggta[cgt]a|t[acg]taccct',
          'agggtaa[cgt]|[acg]ttaccct')
    for f in zip(variants, pool.imap(var_find, variants)):
        print(f[0], f[1])

    subst = {
          'B' : '(c|g|t)', 'D' : '(a|g|t)',   'H' : '(a|c|t)', 'K' : '(g|t)',
          'M' : '(a|c)',   'N' : '(a|c|g|t)', 'R' : '(a|g)',   'S' : '(c|g)',
          'V' : '(a|c|g)', 'W' : '(a|t)',     'Y' : '(c|t)'}
    for f, r in list(subst.items()):
        seq = sub(f, r, seq)

    print()
    print(ilen)
    print(clen)
    print(len(seq))

if __name__=="__main__":
    main()

 make, command-line, and program output logs

Thu, 04 Oct 2012 05:03:43 GMT

MAKE:
mv regexdna.python3 regexdna.py
/usr/local/src/Python-3.3.0/bin/python3.3 -OO -c "from py_compile import compile; compile('regexdna.py')"
0.05s to complete and log all make actions

COMMAND LINE:
/usr/local/src/Python-3.3.0/bin/python3.3 regexdna.py 0 < regexdna-input5000000.txt

PROGRAM OUTPUT:
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
66800214

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