edit.py

import string


VALID_CHARS = set([c for c in string.ascii_letters] + [c for c in string.digits])


class DNA():
	def __init__(self, name='', info='', content=None):
		self.name = name
		self.info = info
		self.content = content

	def __repr__(self):
		return "name: {}\ninfo: {}\ncontent: {}".format(self.name, self.info, self.content)


def add_new_DNA(dna_list, line):
	assert line[0] == '>'
	first_space_idx = line.find(' ')
	if first_space_idx != -1:
		dna_name = line[1:first_space_idx]
		dna_info = line[first_space_idx:].strip()
	else:
		dna_name = line[1:]
		dna_info = ''
	dna_list.append(DNA(name=dna_name, info=dna_info, content=[]))


def add_line_to_DNA(cur_DNA, line):
	for x in line:
		if x in VALID_CHARS:
			cur_DNA.content.append(x)
		elif x == ' ':
			continue
		else:
			raise Exception()


def parse_FASTA(file):
	"""
	Basic state machine for parsing.
	0 = Expecting '>' or empty line.
	1 = Expecting valid string for current DNA or empty line.
	2 = Got at least one string for current DNA. Ready for new DNA
	or continue current DNA.
	"""
	state = 0
	dna_list = []
	for line in file:
		line = line.strip()
		if state == 0:
			if line[0] == '>':
				add_new_DNA(dna_list, line)
				state = 1
			elif line == '':
				continue
			else:
				raise Exception()
		elif state == 1:
			add_line_to_DNA(dna_list[-1], line)
			state = 2
		elif state == 2:
			if line[0] == '>':
				add_new_DNA(dna_list, line)
				state = 1
			else:
				add_line_to_DNA(dna_list[-1], line)
		else:
			raise Exception()
	file.seek(0)
	return dna_list

with open("rosalind_edit.txt") as file:
	dna_list = parse_FASTA(file)

s, t = [x.content for x in dna_list]
gamma = 1
match_cost = 0
mismatch_cost = 1
dists = [j * gamma for j in range(len(s) + 1)]
for i in range(len(t)):
	old_dist = dists[0]
	dists[0] = (i + 1) * gamma
	for j in range(len(s)):
		tmp = min(old_dist + (match_cost if s[j] == t[i] else mismatch_cost), dists[j] + gamma, dists[j + 1] + gamma)
		old_dist = dists[j + 1]
		dists[j + 1] = tmp

print(dists[-1])