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src/p/y/pycogent-HEAD/tests/test_struct/test_pairs_util.py   pycogent(Download)
        #ungapped to gapped
        r = RnaSequence('UC-AG-UC-CG-A-')
        u_to_g = r.gapMaps()[0] 
        #{0: 0, 1: 1, 2: 3, 3: 4, 4: 6, 5: 7, 6: 9, 7: 10, 8: 12}
        ungapped_pairs = Pairs([(0,8),(1,6),(2,5)])
        #gapped to ungapped
        r = RnaSequence('UC-AG-UC-CG-A-')
        g_to_u = r.gapMaps()[1]
        #{0: 0, 1: 1, 3: 2, 4: 3, 6: 4, 7: 5, 9: 6, 10: 7, 12: 8}
        gapped_pairs = Pairs([(0,12),(1,9),(3,7)])

src/c/o/cogent-1.5.3/tests/test_struct/test_pairs_util.py   cogent(Download)
        #ungapped to gapped
        r = RnaSequence('UC-AG-UC-CG-A-')
        u_to_g = r.gapMaps()[0] 
        #{0: 0, 1: 1, 2: 3, 3: 4, 4: 6, 5: 7, 6: 9, 7: 10, 8: 12}
        ungapped_pairs = Pairs([(0,8),(1,6),(2,5)])
        #gapped to ungapped
        r = RnaSequence('UC-AG-UC-CG-A-')
        g_to_u = r.gapMaps()[1]
        #{0: 0, 1: 1, 3: 2, 4: 3, 6: 4, 7: 5, 9: 6, 10: 7, 12: 8}
        gapped_pairs = Pairs([(0,12),(1,9),(3,7)])