In SQL Alchemy you are deleting Objects that you get with a query from the database. This you can do in 2 Ways:
Deleting with query (will issue just one DELETE statement):
session.query(User).filter(User.id==7).delete()
session.commit()
Deleting object instance returned by a query (will issue 2 statements: first SELECT, then DELETE):
obj=session.query(User).filter(User.id==7).first()
session.delete(obj)
session.commit()