performance measurements
Each table row shows performance measurements for this Cython program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 10,000 | 0.04 | 0.04 | ? | 524 | 20% 0% 0% 0% 100% 0% 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 Cython #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
Sun, 23 Apr 2023 09:37:05 GMT MAKE: make[1]: Vstupuje se do adresáře „/home/dundee/work/pybenchmarks/bencher/tmp/regexdna/tmp“ cp regexdna.cython-5.cython `echo regexdna.cython-5.cython | sed 's/cython-..//' | sed 's/.cython//'`.pyx cythonize -3 -bi `echo regexdna.cython-5.cython | sed 's/cython-..//' | sed 's/.cython//'`.pyx Compiling /home/dundee/work/pybenchmarks/bencher/tmp/regexdna/tmp/regexdna.pyx because it changed. [1/1] Cythonizing /home/dundee/work/pybenchmarks/bencher/tmp/regexdna/tmp/regexdna.pyx make[1]: Opouští se adresář „/home/dundee/work/pybenchmarks/bencher/tmp/regexdna/tmp“ 1.53s to complete and log all make actions COMMAND LINE: /usr/bin/python3 -c "import regexdna" 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