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The permutation code in Sage is suboptimal and needs a rewrite. The check for positive input was introduced as a workaround to make the code usable, see http://trac.sagemath.org/ticket/13742 . There you can find that this check can be turned off via

sage: Permutation(range(5),check_input=False)
[0, 1, 2, 3, 4]

This is not recommended and will lead to other problems.