Damian Kao damiankao

damiankao / gist:81b6ebd123b9ccf98e0e47f1ddd3ddd5

Last active January 28, 2021 00:09

	'''
	Naive probabilistic approach backwards engineer the vaccine sequence:
	1. For every codon-position, base, and amino-acid result, calculate a probability of base change.
	2. Apply this probability to the viral sequence and generate a vaccine sequence.
	3. Compare the generated vaccine sequence to the known vaccine sequence and check for % match.

	This code is in reference to:
	https://berthub.eu/articles/posts/part-2-reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/

	Requires python3

damiankao / py-coordinateOperations

Created December 12, 2015 12:17

Python functions to find union of multiple coordinates and intersection of multiple coordinates


	def tileCoords(coords):
	formatCoords = []
	for coord in coords:
	coord = [int(coord[0]),int(coord[1])]

	formatCoords.append(('s',min(coord)))
	formatCoords.append(('e',max(coord)))

	formatCoords.sort(key = lambda x : x[0], reverse = True)

damiankao / py-bwt.py

Last active December 12, 2015 12:29

Simple implementation of Burrows-Wheeler transformation in python

	def encode(inputStr):
	rotations = [inputStr[i:] + inputStr[:i] for i in range(len(inputStr))]
	rotations.sort()
	encodedStr = [x[-1] for x in rotations]
	index = rotations.index(inputStr)
	return (''.join(encodedStr), index)

	def decode(encodedStr, index):
	rotations = [encodedStr[i] for i in range(len(encodedStr))]
	for i in range(len(encodedStr) - 1):

damiankao / gist:10324781

Created April 9, 2014 22:22