large_csv_to_sqlite.py

# This is a workaround snippet for reading very large CSV that exceed the
# machine's memory and dump it into an SQLite database using pandas.
#
# Sebastian Raschka, 2015
#
# Tested in Python 3.4.2 and pandas 0.15.2 

import pandas as pd
import sqlite3
from pandas.io import sql
import subprocess

# In and output file paths
in_csv = '../data/my_large.csv'
out_sqlite = '../data/my.sqlite'

table_name = 'my_table' # name for the SQLite database table
chunksize = 100000 # number of lines to process at each iteration

# columns that should be read from the CSV file
columns = ['molecule_id','charge','db','drugsnow','hba','hbd','loc','nrb','smiles']

# Get number of lines in the CSV file
nlines = subprocess.check_output(['wc', '-l', in_csv])
nlines = int(nlines.split()[0]) 

# connect to database
cnx = sqlite3.connect(out_sqlite)

# Iteratively read CSV and dump lines into the SQLite table
for i in range(0, nlines, chunksize):  # change 0 -> 1 if your csv file contains a column header
    
    df = pd.read_csv(in_csv,  
            header=None,  # no header, define column header manually later
            nrows=chunksize, # number of rows to read at each iteration
            skiprows=i)   # skip rows that were already read
    
    # columns to read        
    df.columns = columns

    sql.to_sql(df, 
                name=table_name, 
                con=cnx, 
                index=False, # don't use CSV file index
                index_label='molecule_id', # use a unique column from DataFrame as index
                if_exists='append') 
cnx.close()