Apparently some csv output implementation somewhere truncates field separators from the right on the last row and only the last row in the file when the fields are null.
Basically you only know you've run out after you've run out. So you could wrap the reader iterator, e.g. as follows:
def isLast(itr):
old = itr.next()
for new in itr:
yield False, old
old = new
yield True, old
and change your code to:
for line_num, (is_last, row) in enumerate(isLast(reader)):
if not is_last: assert len(row) == len(header)
etc.