def nt_pos_shift(nt_pos, AAshift):
	"""
		Modify nucleotide positions in our alignment to actual positions in the real wild-type sequence.

		nt_pos : base number of wild type sequence start at 1, not python 0
		AAshift : the residue corresponding to the wild type base starting at 1
	"""
	if (nt_pos < 1):
		raise Exception('Bases provided must start at 1')
	return nt_pos + (AAshift - 1) * 3