performance measurements

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

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
10,0000.130.14?501  50% 7% 57% 0%
10,0000.130.13?501  0% 7% 100% 0%
10,0000.130.13?501  7% 93% 0% 0%

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

 regex-dna PyPy #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.read()
    write = stdout.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)))) + 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)) + b'\n')
    write(bytes(str(clen)) + b'\n')
    write(bytes(str(len(seq))) + b'\n')

main()

 make, command-line, and program output logs

Thu, 26 Apr 2018 16:46:27 GMT

COMMAND LINE:
/usr/bin/pypy regexdna.pypy-5.pypy 0 < regexdna-input10000.txt

PROGRAM OUTPUT:
agggtaaa|tttaccct 0
[cgt]gggtaaa|tttaccc[acg] 3
a[act]ggtaaa|tttacc[agt]t 9
ag[act]gtaaa|tttac[agt]ct 8
agg[act]taaa|ttta[agt]cct 10
aggg[acg]aaa|ttt[cgt]ccct 3
agggt[cgt]aa|tt[acg]accct 4
agggta[cgt]a|t[acg]taccct 3
agggtaa[cgt]|[acg]ttaccct 5

101745
100000
133640

Revised BSD license

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