You can use the strip() function to remove trailing (and leading) whitespace; passing it an argument will let you specify which whitespace:
for i in range(len(lists)):
grades.append(lists[i].strip('\n'))
It looks like you can just simplify the whole block though, since if your file stores one ID per line grades is just lists with newlines stripped:
Before
lists = files.readlines()
grades = []
for i in range(len(lists)):
grades.append(lists[i].split(","))
After
grades = [x.strip() for x in files.readlines()]
(the above is a list comprehension)
Finally, you can loop over a list directly, instead of using an index:
Before
for i in range(len(grades)):
# do something with grades[i]
After
for thisGrade in grades:
# do something with thisGrade