Big SELECT optimization

Question

我在Python中使用SQLite作为一个大型文件管理系统。我有一个大的平面文件(1亿行)，我想用3列(整数)的值来排序，这样我就可以迭代和做一些计算。

我使用了一个大SELECT ... ORDER BY的SQLite(在一列上有一个索引)。由于这个大SELECT对内存的要求太高，我需要调用它几次(OFFSET和LIMIT)。

我可以使用Linux排序，但我希望它是独立于平台的。它工作得很好(只要正确设置了PRAGMA)，但是速度很慢。如何优化呢?

命令如下:

PRAGMA journal_mode = OFF
PRAGMA synchronous = 0
PRAGMA locking_mode = EXCLUSIVE
PRAGMA count_change = OFF
PRAGMA temp_store = 2
CREATE TABLE tmpTranscripts_arm_3R_transcripts (id INTEGER PRIMARY KEY, name varchar(255), chromosome varchar(255), start int(11), end int(11), direction tinyint(4), tags varchar(1023), bin int(11), exons varchar(10000))
CREATE INDEX 'iTranscript_arm_3R_14943' ON 'tmpTranscripts_arm_3R_transcripts' (start, end, direction)
INSERT INTO tmpTranscripts_arm_3R_transcripts (name, chromosome, start, end, direction, tags, bin, exons) VALUES ('SRR060644.1', 'arm_3R', 11450314, 11450337, -1, 'feature=transcript;bestRegion=(self);nbGaps=0;nbMismatches=0;ID=SRR060644.1;identity=100.0', 300011450, '')
(this, more than 10 millions times)
SELECT * FROM tmpTranscripts_arm_3R_transcripts ORDER BY start, end, direction LIMIT 0, 10000
(this, as much as needed)

Answer 1

我已经编写了一些示例脚本，用于创建数据库并遍历其所有元素。看起来它比你在评论里写的要快得多。您确定数据库访问是瓶颈吗?也许在你的脚本中你做了更多的事情，这花费了很多时间。

我检查了2个数据库SQLite和MongoDB与500万个项目。对于SQLite，插入所有行大约需要1200秒，选择行大约需要300秒。MongoDB的速度更快，插入大约需要400秒，而选择不到100秒。

请检查你的代码与我的样本，检查你的选择是否相似。我使用游标代替限制/偏移。如果这仍然没有帮助，那么我认为MongoDB值得一试。它有一个缺点——它需要64位操作系统来支持大型数据库(如您的数据库)。如果你以前用过它，这里是windows的最短安装指南:

• 从http://www.mongodb.org/downloads下载并解压MongoDB for windows 64位
• 运行"mongod.exe——dbpath ."
• python 2的下载模块。X从http://pypi.python.org/pypi/pymongo/或python 3。x来自http://pypi.python.org/pypi/pymongo3/
• 运行脚本

这是我的蟒蛇。

import sqlite3
from time import time
conn = sqlite3.connect('test.dbase')
c = conn.cursor()
c.execute("""PRAGMA journal_mode = OFF""")
c.execute("""PRAGMA synchronous = 0""")
c.execute("""PRAGMA locking_mode = EXCLUSIVE""")
c.execute("""PRAGMA count_change = OFF""")
c.execute("""PRAGMA temp_store = 2""")
c.execute("""CREATE TABLE tmpTranscripts_arm_3R_transcripts (id INTEGER PRIMARY KEY, name varchar(255), chromosome varchar(255), start int(11), end int(11), direction tinyint(4), tags varchar(1023), bin int(11), exons varchar(10000))""")
c.execute("""CREATE INDEX 'iTranscript_arm_3R_14943' ON 'tmpTranscripts_arm_3R_transcripts' (start, end, direction)""")
t1 = time()
for i in range(0, 5000000):
    c.execute("""INSERT INTO tmpTranscripts_arm_3R_transcripts (name, chromosome, start, end, direction, tags, bin, exons) VALUES ('SRR060644.1', 'arm_3R', %d, %d, %d, 'feature=transcript;bestRegion=(self);nbGaps=0;nbMismatches=0;ID=SRR060644.1;identity=100.0', 300011450, '')""" % ((i+123)%352, (i+523)%422, (i+866)%536))
    if(not i%10000):
        print("Insert:", i)
t2 = time()
print("Insert time", t2-t1)
conn.commit()
t1 = time()
c.execute("""SELECT * FROM tmpTranscripts_arm_3R_transcripts ORDER BY start, end, direction""")
i = 0
for row in c:
    a = row[0]
    if(not i%10000):
        print("Get:", i, row)
    i+=1
t2 = time()
print("Sort time", t2-t1)
c.close()

和MongoDB

from pymongo import Connection
from pymongo import ASCENDING, DESCENDING
from time import time
connection = Connection()
connection = Connection('localhost', 27017)
db = connection['test-database']
collection = db['test-collection']
posts = db.posts
posts.create_index([("start", ASCENDING), ("end", ASCENDING), ("direction", ASCENDING)])
t1 = time()
for i in range(0, 5000000):
    post = { "name": 'SRR060644.1',
            "chromosome": 'arm_3R',
            "start": (i+123)%352,
            "end": (i+523)%422,
            "direction": (i+866)%536,
            "tags": 'feature=transcript;bestRegion=(self);nbGaps=0;nbMismatches=0;ID=SRR060644.1;identity=100.0',
            "bin": 300011450,
            "exons": ''}
    posts.insert(post)
    if(not i%10000):
        print("Insert:", i)
t2 = time()
print("Insert time", t2-t1)
t1 = time()
i = 0
for post in posts.find().sort([("start", ASCENDING), ("end", ASCENDING), ("direction", ASCENDING)]):
    if(not i%10000):
        print("Get:", i, post)
    i+=1
t2 = time()
print("Sort time", t2-t1)