comparing two large csv file and writing another one with python

I am trying to compare two large csv files containing chemicals data.

the first one, "file1" is 14 Mb (which is not so heavy), but the second one, "file2" is 3Go (47798771 lines).

here a sample of file 1 (we'll focus on the fourth column, which contains inchikeys) :

MFCD00134034    7440-42-8   B   UORVGPXVDQYIDP-UHFFFAOYSA-N
MFCD01745487    64719-89-7  B1BBBB(BBBBB1[Li])[Li]  XZXJQLAKEUKXOT-UHFFFAOYSA-N
MFCD01310566    19287-45-7  BB  QSJRRLWJRLPVID-UHFFFAOYSA-N
MFCD00011323    10035-10-6  Br  CPELXLSAUQHCOX-UHFFFAOYSA-N
        N(CCNCCCCCCCCCCNCCN(CC)CC)(CC)CC    PISAWRHWZGEVPP-UHFFFAOYSA-N
MFCD01744969    137638-86-9 O(C(=O)C(c1ccccc1)c1ccccc1)c1cc2c(C[C@H]3N(CC[C@]2(C)C3C)Cc2ccccc2)cc1  CIRJJEXKLBHURV-MAYWEXTGSA-N
        O(CCCN1CCCC1)c1ccc(NC(=Nc2ccccc2)c2ccccc2)cc1   KETUBKLQEXFJBX-UHFFFAOYSA-N
MFCD01694581    3810-31-9   S(CCN(CCSC(N)=N)CCSC(N)=N)C(N)=N    GGDUORJVTMUGNU-UHFFFAOYSA-N
MFCD06794992    60066-94-6  Brc1cc(C(=O)c2ncccc2)c(NC(=O)CNC(=O)[C@@H](N)CCCCN)cc1  NVOGGKXDMDDFEG-HNNXBMFYSA-N
MFCD06794980    60066-98-0  Brc1cc(C(=O)c2ncccc2)c(NC(=O)CNC(=O)[C@@H](N)CCCNC(N)=N)cc1 LFCYDGUHINTBOJ-AWEZNQCLSA-N

file 2 :

lat_chemical_id stereo_chemical_id  source_cid  inchikey
CID100000001    CID000000001    1   RDHQFKQIGNGIED-UHFFFAOYSA-N
CID100000010    CID000000010    10  AUFGTPPARQZWDO-UHFFFAOYSA-N
CID100000100    CID000000100    100 UTIBHEBNILDQKX-UHFFFAOYSA-N
CID100001000    CID000001000    1000    ULSIYEODSMZIPX-UHFFFAOYSA-N
CID100010000    CID000010000    10000   ZPIFKCVYZBVZIV-UHFFFAOYSA-N
CID100100000    CID000100000    100000  SPTBIJLJJBZGDY-UHFFFAOYSA-N
CID101000000    CID001000000    1000000 XTNVYACQOFUTNH-UHFFFAOYSA-N
CID110000000    CID010000000    10000000    WUGPGGSZFRVGGA-UHFFFAOYSA-N
CID110000001    CID010000001    10000001    ANOUMYXLUIDQNL-UHFFFAOYSA-N

My goal is to compare the inchikeys, fourth row in boths files,to see if they are the same. Then when its the case, extract all info (from both files)and write them i third one.

here's my (naive) code :

#!/usr/bin/env python
#-*- coding: utf-8 -*-
######################
import numpy as np
import argparse 
import csv 
#################################


def compare(tab_data_inchik,stitch,output):
    dt = open(tab_data_inchik, 'rb')
    st = open(stitch,'rb')
    out = open(output,'wb')
    data = csv.reader(dt, delimiter = '\t')
    database = csv.reader(st, delimiter = '\t')
    result = csv.writer(out, delimiter = '\t')
    for line in data:
        for row in database:
            if line[3] == row[3]:
                result.writerow((line[0],line[1],line[2],row[0],row[1],row[2],row[3]))        

    dt.close()
    st.close()
    out.close()

##############################""
if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument("tsv1", help = "Pr Data")
    parser.add_argument("tsv2", help = "Database")
    parser.add_argument("output", help = "output file")
    args=parser.parse_args()

    compare(args.tsv1,args.tsv2,args.output)

It seems that, the program does not even reach the second line of the database loop, I guess it's because the file is to large and my method is bot optimized. Maybe I should use numpy.where() but I don't see how.

Is there a way to get the information without the double loop ? Thanks in advance.