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 |
|---|---|---|---|---|---|
| 10,000 | 0.08 | 0.06 | ? | 801 | 57% 50% 14% 0% 25% 17% 29% 17% |
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 3.3.1 (default, Apr 11 2013, 12:45:45) [GCC 4.7.2] on linux
Notice that sought sequences (GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT) newer overlap and create new function find_seq() with built-in function count(). Previous program iterated all data in function sort_seq() - char by char.
Improved gen_func() - removed "if" statement and used defaultdict() function
BUT skips the sequence generation in the sequence finder step. def find_seq(seq, nucleo): count = seq.count(nucleo) return nucleo, count
k-nucleotide Python 3 #2 program source code
# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# modified by jacek2v: few changes in algorytm, added multiprocessing, used str.count (nucleo newer overlapping)
from sys import stdin
from collections import defaultdict
from multiprocessing import Process, Pool, cpu_count
def gen_freq(seq, frame):
frequences = defaultdict(int)
ns = len(seq) + 1 - frame
for ii in range(ns):
frequences[seq[ii:ii + frame]] += 1
return ns, frequences
def sort_seq(seq, length):
n, frequences = gen_freq(seq, length)
#l = sorted(frequences.items(), reverse=True, key=lambda (seq,freq): (freq,seq))
l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1],seq_freq[0]))
return [(st, 100.0*fr/n) for st, fr in l]
def find_seq(seq, nucleo):
count = seq.count(nucleo)
return nucleo, count
def load():
for line in stdin:
if line[0:3] == ">TH":
break
seq = []
for line in stdin:
if line[0] in ">;":
break
seq.append( line[:-1] )
return seq
def main():
nucleos = "GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT"
sequence = "".join(load()).upper()
plres = []
pl = Pool(processes=cpu_count() + 1)
for nl in 1,2:
plres.append(pl.apply_async(sort_seq, (sequence, nl, )))
for se in nucleos.split():
plres.append(pl.apply_async(find_seq, (sequence, se, )))
pl.close()
pl.join()
for ii in 0,1:
print('\n'.join("%s %.3f" % (st, fr) for st,fr in plres[ii].get()))
print('')
for ii in range(2, len(nucleos.split()) + 2):
print("%d\t%s" % (plres[ii].get()[1], plres[ii].get()[0]))
main()
make, command-line, and program output logs
Sun, 30 Jul 2023 10:51:27 GMT COMMAND LINE: /usr/bin/python3 knucleotide.python3-2.python3 0 < knucleotide-input10000.txt PROGRAM OUTPUT: A 30.284 T 29.796 C 20.312 G 19.608 AA 9.212 AT 8.950 TT 8.948 TA 8.936 CA 6.166 CT 6.100 AC 6.086 TC 6.042 AG 6.036 GA 5.968 TG 5.868 GT 5.798 CC 4.140 GC 4.044 CG 3.906 GG 3.798 562 GGT 152 GGTA 15 GGTATT 0 GGTATTTTAATT 0 GGTATTTTAATTTATAGT