khmer-perf-eval.py

from __future__ import print_function
from collections import defaultdict
import argparse
import khmer
import statistics
import sys
import time

allocators = {
    'ct': khmer.Counttable,
    'cg': khmer.Countgraph,
    'nt': khmer.Nodetable,
    'ng': khmer.Nodegraph,
}

def timeload(sketch, infile, query=False):
    start = time.time()
    nr, nk = sketch.consume_seqfile(infile)
    elapsed = time.time() - start

    if query:
        for n, read in enumerate(khmer.ReadParser(infile)):
            for kmer in sketch.get_kmers(read.sequence):
                assert sketch.get(kmer) == 0, sketch.get(kmer)
            if n > 10000:
                break

    return elapsed

parser = argparse.ArgumentParser()
parser.add_argument('--memory', type=float, default=4e8)
parser.add_argument('--type', choices=allocators.keys(), default='ct')
parser.add_argument('--doquery', action='store_true')
parser.add_argument('infile')
args = parser.parse_args()

alloc = allocators[args.type]
sketch = alloc(25, args.memory / 4, 4)
elapsed = timeload(sketch, args.infile, query=args.doquery)
print('sketch={} insert={} time={:.2f}'.format(args.type, not args.doquery, elapsed))

output-hash-no-insert.txt

sketch=ct insert=False time=379.35
sketch=ct insert=False time=379.44
sketch=ct insert=False time=378.06

sketch=cg insert=False time=72.24
sketch=cg insert=False time=72.49
sketch=cg insert=False time=72.60

output-master.txt

sketch=ct insert=True time=706.32
sketch=ct insert=True time=708.33
sketch=ct insert=True time=717.29

sketch=cg insert=True time=451.87
sketch=cg insert=True time=451.94
sketch=cg insert=True time=452.96