Python hamming Examples

Example #1

File: BA1H_PatternMatchWithMismath.py Project: bioJain/python_Bioinformatics

def PatternMatchWithMis(pattern, text, d):
	startingIndex = []
	for i in range(len(text)-len(pattern)+1):
		pattern2 = text[i:i+len(pattern)]
		if hamming(pattern, pattern2) <= d:
			startingIndex.append(i)
	return startingIndex

Example #2

File: BA1I_FreqWordWithMis.py Project: bioJain/python_Bioinformatics

def Neighbors(pattern, d):
	if d == 0:
		return pattern
	if len(pattern) == 1:
		return ['A', 'C', 'G', 'T']
	Neighborhood = []
	SuffixNeighbors = Neighbors(pattern[1:], d)
	for text in SuffixNeighbors :
		if hamming(pattern[1:], text) < d :
			for nt in ['A', 'C', 'G', 'T']:
				Neighborhood.append(nt+text)
		else :
			Neighborhood.append(pattern[0]+text)
	return Neighborhood