This is an older thread, but I just wanted to dump my workaround solution here. I initially tried the chunksize parameter (even with quite small values like 10000), but it didn't help much; had still technical issues with the memory size (my CSV was ~ 7.5 Gb).
Right now, I just read chunks of the CSV files in a for-loop approach and add them e.g., to an SQLite database step by step:
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 %s' % in_csv, shell=True)
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):
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()
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