Functions for computing properties of simulated partial digests of DNA.

I have provided 3 functions: deltaX, BruteForcePDP and AnotherBruteForcePDP. deltaX(sites) will compute the sizes of all the possible fragments of a partial digest of a sequence given a list of restriction sites.

>>> from partial import *
>>> deltaX([0, 1, 3, 6, 10])
[1, 2, 3, 3, 4, 5, 6, 7, 9, 10]

BruteForcePDP(L, n) computes the list of restriction sites if given a valid list of fragment sizes.

>>> BruteForcePDP([1, 2, 3, 3, 4, 5, 6, 7, 9, 10], 5)
[0, 1, 3, 6, 10]

The function AnotherBruteForcePDP does the same as the first, but iterates over the frangments sizes in L instead of over all the integers. It's much faster when the max(L) is large. For example

>>> from partial import *
>>> X=[0,1,3,6,500,3000]
>>> L = deltaX(X)
>>> BruteForcePDP(L,6)
[0, 1, 3, 6, 500, 3000]

Takes 47 seconds on my computer, but AnotherBruteForcePDP only takes 0.001 seconds.