Quick Start

Test the C++ interface, follow these steps:

cd ../examples/
# Default install directory: ../build/
make

You can use the following command:

./exe_SKETCH_ALGORITHM FILE_LIST threshold(0.05) thread_num

This is a quick example of how to use rabbitsketch for large scale genome similarity analysis.

import rabbitsketch as sketch
import fastx,time
import pymp
from multiprocessing import Manager,Queue
import math
import numpy as np
THREAD_NUM = 64
file_list = []
t1 = time.time()
half_k = 10
half_subk = 6
drlevel = 3
info = sketch.SketchInfo()
info.half_k = half_k
info.half_subk = half_subk
info.drlevel = drlevel

file_path = "/PATH/L3K10.shuf"
kssd_para = sketch.kssd_parameter_t(half_k, half_subk, drlevel, file_path)
vkssd = pymp.shared.list()
with open('GENOME.LIST', "r") as bact1000:
    for genomefile in bact1000:
        genomefile = genomefile.strip()
        file_list.append(genomefile)
print("length of file is:", len(file_list))
with pymp.Parallel(THREAD_NUM) as p:
    for index in p.xrange(0, len(file_list)):
            kssd = sketch.Kssd(kssd_para)
            kssd.fileName = file_list[index]
            for name, seq, qual in fastx.Fastx(file_list[index]):
                kssd.update(seq)
            kssd_lite = kssd.toLite()
            vkssd.append(kssd_lite)

print(len(vkssd))
info.genomeNumber = len(vkssd)
sketch.save_sketches(vkssd, info, "pysketch")

t2 = time.time()
print("sketch time is :", t2-t1)

sketch.trans_sketches(vkssd, info, "pysketch.dict", "pysketch.index", THREAD_NUM)
t3 = time.time()
print("trans time is :", t3-t2)

sketch.index_dict(vkssd, info, "pysketch", "pysketch.dist", 20, 0.05, 0, THREAD_NUM)
t4 = time.time()
print("dist time is :", t4-t3)