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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	0.24	0.25	276	424	0% 0% 4% 96%
500,000	2.15	2.15	11,352	424	0% 0% 1% 100%
5,000,000	21.13	21.14	194,612	424	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, 12:56:47)
[GCC 4.7.2] on linux

 regex-dna Python 3 #5 program source code

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

from sys import stdin,stdout
from re import sub, findall

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

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

    variants = (
          b'agggtaaa|tttaccct',
          b'[cgt]gggtaaa|tttaccc[acg]',
          b'a[act]ggtaaa|tttacc[agt]t',
          b'ag[act]gtaaa|tttac[agt]ct',
          b'agg[act]taaa|ttta[agt]cct',
          b'aggg[acg]aaa|ttt[cgt]ccct',
          b'agggt[cgt]aa|tt[acg]accct',
          b'agggta[cgt]a|t[acg]taccct',
          b'agggtaa[cgt]|[acg]ttaccct')
    for f in variants:
        write(f + b' ' +bytes(str(len(findall(f, seq))),encoding='latin1') + b'\n')

    subst = {
          b'B' : b'(c|g|t)', b'D' : b'(a|g|t)',   b'H' : b'(a|c|t)', b'K' : b'(g|t)',
          b'M' : b'(a|c)',   b'N' : b'(a|c|g|t)', b'R' : b'(a|g)',   b'S' : b'(c|g)',
          b'V' : b'(a|c|g)', b'W' : b'(a|t)',     b'Y' : b'(c|t)'}
    for f, r in subst.items():
        seq = sub(f, r, seq)
    write(b'\n')
    write(bytes(str(ilen),encoding='latin1') + b'\n')
    write(bytes(str(clen),encoding='latin1') + b'\n')
    write(bytes(str(len(seq)),encoding='latin1') + b'\n')

main()

 make, command-line, and program output logs

Sat, 29 Sep 2012 23:03:23 GMT

MAKE:
mv regexdna.python3-5.python3 regexdna.python3-5.py
0.01s to complete and log all make actions

COMMAND LINE:
/usr/local/src/Python-3.3.0/bin/python3.3 regexdna.python3-5.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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