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.