I am trying to update my text file by matching the first column to another updated file's first column, after match it, it will update the old file. Here is my old file: Name Chr Pos ind1 in2 in3 ind4 foot 1 5 aa bb cc ford 3 9 bb cc 00 fake 3 13 dd ee ff fool 1 5 ee ff gg fork 1 3 ff gg ee Here is the new file: Name Chr Pos foot 1 5 fool 2 5 fork 2 6 ford 3 9 fake 3 13 The updated file will be like: Name Chr Pos ind1 in2 in3 ind4 foot 1 5 aa bb cc fool 2 5 ee ff gg fork 2 6 ff gg ee ford 3 9 bb cc 00 fake 3 13 dd ee ff Here is my code: #!/usr/bin/env python import sys inputfile_1 = sys.argv[1] inputfile_2 = sys.argv[2] outputfile = sys.argv[3] inputfile1 = open(inputfile_1, 'r') inputfile2 = open(inputfile_2, 'r') outputfile = open(outputfile, 'w') ind = inputfile1.readlines() cm = inputfile2.readlines()[1:] outputfile.write(ind[0]) #add header for i in ind: i = i.split() for j in cm: j = j.split() if j[0] == i[0]: outputfile.writelines(j[0:3] + i[3:]) inputfile1.close() inputfile2.close() outputfile.close() When I ran it, it returned a single column rather than the format i wanted, any suggestions? Thanks!