command, i can't tell python to only get the next line of file 1, and keep the line of file 2, and thus are unable to make a merge sort
No you can.
line1 = file1.readline()
line2 = file2.readline()
while file1_not_at_end and file2_not_at_end:
if line1 < line2:
file3.write(line1)
line1 = file1.readline()
else:
file3.write(line2)
line2 = file2.readline()
# merge file 1 into file 3
# merge file 2 into file 3