加速sqlite3数据库搜索

Question

I"m new to databases and just wrote my first code using sqlite3 . It does the job, but is running extremely slowly and I'm hoping to get some advice regarding how to speed things up.

Right now my code looks something like this:

For Line in File:
   Line= Line.strip('\n').split('\n')
   Location = int(Line[1])
   MChr = Line[0]
cur = db.execute('''SELECT Start, End, Chr, Feature1, Feature2, Feature3, Feature4, FROM DataBase
                    WHERE Start <= ? AND End >= ? AND Chr == ?''', (Location, Location, MChr))
for (Start, Stop, Chr, Feature1, Feature2, Feature3, Feature4) in cur:
    if Feature1 == "A string":
        do something....
    if Feature2 == "A string":
        do something....

My database is a little over one million entries which is probably why my program is running slow but I was wondering if there is a way to make the search more efficient to circumvent having to run through all million for every line. (Perhaps first pull out all matching Chrs?)

Answer 1

You should index your db:

http://www.sqlite.org/lang_createindex.html

This should speed things up.

Answer 2

Create indexes on the columns in question. If your table name is DataBase , then try something like:

db.execute('''CREATE UNIQUE INDEX Start_index ON `DataBase` (`Start`(64))''')
db.execute('''CREATE UNIQUE INDEX End_index ON `DataBase` (`End`(64))''')
db.execute('''CREATE UNIQUE INDEX Chr_index ON `DataBase` (`Chr`(64))''')