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src/c/o/cogent-1.5.3/cogent/struct/knots.py   cogent(Download)
    # preprocess
    raw_pairs = Pairs(pairs)
    if raw_pairs.hasConflicts():
        raise ValueError("Cannot handle pairs with conflicts")
    p = raw_pairs.directed()
    if not p:
        return PairedRegions()
    if p.hasConflicts():
        raise ValueError("Cannot handle base pair conflicts")
    clean_pairs = p.directed()

src/p/y/pycogent-HEAD/cogent/struct/knots.py   pycogent(Download)
    # preprocess
    raw_pairs = Pairs(pairs)
    if raw_pairs.hasConflicts():
        raise ValueError("Cannot handle pairs with conflicts")
    p = raw_pairs.directed()
    if not p:
        return PairedRegions()
    if p.hasConflicts():
        raise ValueError("Cannot handle base pair conflicts")
    clean_pairs = p.directed()