There are tasks that require mapping some features over an array (i.e. chromosome). Here, I post a simple class in python that can store features over an array. It allows easy additions of the values to it. You need to have numpy installed in order to run it. A simple use is presented. Please remember, it follows the python rules it means the system is zero based and the last position is not included (you need to add 1 to include the last number – in other words, the interval is open on the right or right-open).
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import numpy as np class GenomicArray(): def __init__(self, size): self.size = size self.store = np.zeros(self.size) def chunk_add(self, s, e, val): self.s = s self.e = e self.val = val self.store[self.s:self.e] += self.val return self.store #length of array i.e. for human chromosome1 chr1_length = 247249719 #initialize chr1_array chr1_array = GenomicArray(chr1_length) chr1_array.chunk_add(3,5,10) chr1_array.chunk_add(4,10,20) #see that values changed print chr1_array.store[0:20] |