cthoyt/blast_problem.py

## blast_problem.py
#!/usr/bin/env python
# Author: Charlie Hoyt

import itertools as itt

s = {
    ('A','A'): 5,
    ('A','R'): -2,
    ('A','N'): -1,
    ('A','D'): -2,
    ('R','A'): -2,
    ('R','R'): 7,
    ('R','N'): -1,
    ('R','D'): -2,
    ('N','A'): -1,
    ('N','R'): -1,
    ('N','N'): 7,
    ('N','D'): 2,
    ('D','A'): -2,
    ('D','R'): -2,
    ('D','N'): 2,
    ('D','D'): 8
}

alphabet = "ARND"
target ="RRDNARD"

substring_len = 4
threshold = 3
valid_count = 0

# iterate over all possible elements of alphabet^substring_len
for perm in itt.product(alphabet, repeat=substring_len):
    # start with worst possible score
    max_score = min(s.values()) * substring_len

    # slide window and calculate score for each
    for i in range(len(target) - substring_len):
        score = sum(s[matching] for matching in zip(perm, target[i:i + substring_len]))
        if max_score < score:
            max_score = score

    if threshold <= max_score:
        print(''.join(perm), max_score)
        valid_count += 1

print(valid_count)
# Answer: 238
	#!/usr/bin/env python
	# Author: Charlie Hoyt

	import itertools as itt

	s = {
	('A','A'): 5,
	('A','R'): -2,
	('A','N'): -1,
	('A','D'): -2,
	('R','A'): -2,
	('R','R'): 7,
	('R','N'): -1,
	('R','D'): -2,
	('N','A'): -1,
	('N','R'): -1,
	('N','N'): 7,
	('N','D'): 2,
	('D','A'): -2,
	('D','R'): -2,
	('D','N'): 2,
	('D','D'): 8
	}

	alphabet = "ARND"
	target ="RRDNARD"

	substring_len = 4
	threshold = 3
	valid_count = 0

	# iterate over all possible elements of alphabet^substring_len
	for perm in itt.product(alphabet, repeat=substring_len):
	# start with worst possible score
	max_score = min(s.values()) * substring_len

	# slide window and calculate score for each
	for i in range(len(target) - substring_len):
	score = sum(s[matching] for matching in zip(perm, target[i:i + substring_len]))
	if max_score < score:
	max_score = score

	if threshold <= max_score:
	print(''.join(perm), max_score)
	valid_count += 1

	print(valid_count)
	# Answer: 238