MnkzaQgz

1accession   accession.version   taxid   gi
2V00184      V00184.1            44689   7184
3V00185      V00185.1            44689   7186
4V00187      V00187.1            44689   7190
5X07806      X07806.1            7227    8179 
6     
7import sqlite3
8import time
9
10start = time.time()
11
12connection = sqlite3.connect("test.sqlite")
13cursor = connection.cursor()    
14
15cursor.execute("""
16    CREATE TABLE IF NOT EXISTS map (
17        accession TEXT PRIMARY KEY,
18        accession_version TEXT,
19        taxid TEXT, gi TEXT
20    )""")
21
22
23def read_large_file(f):
24    """Generator for the file"""
25    for l in f:
26        yield l.strip().split()
27
28with open("test_file.map", "r") as f:
29    next(f)  # ignore header
30    cursor.executemany("INSERT INTO map VALUES (?, ?, ?, ?)", read_large_file(f))
31
32cursor.close()
33connection.commit()
34connection.close()
35
36print(time.time() - start)