I read several examples that show how pymysql "select in" should work. So, this example works just fine:
sql_select = 'SELECT a.user_id, AVG(a.rcount) AS \'average\' ' \
'FROM (SELECT user_id, item_id, count(*) AS rcount ' \
'FROM submission AS qsm ' \
'JOIN metadata as qm ' \
'ON qsm.item_id = qm.id ' \
'WHERE qsm.item_id NOT IN (1, 2, 5, 6, 7, 147, 148) ' \
'AND DATE(FROM_UNIXTIME(submission_time)) BETWEEN %s AND %s ' \
'AND qm.type != \'survey\' ' \
'GROUP BY user_id, item_id ' \
'ORDER BY user_id) a ' \
'GROUP BY a.user_id'
args = [course_start, course_end]
cur.execute(sql_select, args)
But, I would also like to add another argument for this "NOT IN" part. The problem here is that this list is variable, so not quite sure how to handle this one.