How can I do sliding window on DNA sequence alignment?
How can I do sliding window on dna sequence alignment dot matrix? I was trying to do something like this, but I don't know how to end this.
import numpy as np import matplotlib.pyplot as plt X = "" Y = "" X = np.array(list(X)) Y = np.array(list(Y)) c = X == Y[:, None] print(c) for p in c: t = 0 while p == True: t = t + 1 if t < 7:
And I was trying to use this code, I found this on internet and I want to try this and see how it works. But it doesn't and I don't know why.
def simpleDotPlot(s1, s2, wsize): row = 0 vWindow =  #vertical windows for c2 in s2: vWindow.append(c2) if row>=wsize-1: if row>=wsize: vWindow.pop(0) #remove the first item. print (vWindow), hWindow =  col = 0 for c1 in s1: hWindow.append(c1) if col>=wsize - 1: if col>=wsize: hWindow.pop(0) if hWindow==vWindow: print ('X'), else: print ("."), col += 1 for c in range(wsize-1): print ('.'), print row+=1 simpleDotPlot("dorothyhodgkin", "dorothycrowfoothodgkin",1)
I want to have somrting that can filter the noise in the alignment, that I can see just the main alignment bigger than 1. Thank you for any help,