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src/c/o/cogent-1.5.3/tests/test_core/test_alignment.py   cogent(Download)
        seq_exp = array([[1,1,1,1],[0,3,1,0],[1,0,2,1]])
        pos_exp = array([[1,1,1,0],[0,2,0,1],[0,0,3,0],[1,1,0,1]])
        self.assertEqual(da._get_freqs(index=1), pos_exp)
        self.assertEqual(da._get_freqs(index=0), seq_exp)
 

src/p/y/pycogent-HEAD/tests/test_core/test_alignment.py   pycogent(Download)
        seq_exp = array([[1,1,1,1],[0,3,1,0],[1,0,2,1]])
        pos_exp = array([[1,1,1,0],[0,2,0,1],[0,0,3,0],[1,1,0,1]])
        self.assertEqual(da._get_freqs(index=1), pos_exp)
        self.assertEqual(da._get_freqs(index=0), seq_exp)