def q7():
x = "ABCABC"
y = "ABCABC"
sm = soln.build_scoring_matrix("ABC-", 2, 1, 0)
print sm
# global
am = soln.compute_alignment_matrix(x, y, sm, True)
print soln.compute_global_alignment(x, y, sm, am)
def check_spelling(checked_word, dist, word_list):
answer = set()
letters = list("qwertyuiopasdfghjklzxcvbnm")
scor_matrix = p.build_scoring_matrix(letters, 2, 1, 0)
for word in word_list:
align_matrix = p.compute_alignment_matrix(checked_word, word,
scor_matrix, True)
score = p.compute_global_alignment(checked_word, word, scor_matrix,
align_matrix)[0]
edit_distance = len(word) + len(checked_word) - score
if edit_distance <= dist:
answer.add(word)
return answer
def q7():
seq_x = "kqistian"
seq_y = "kristian"
scor_matrix = p.build_scoring_matrix(
["a", "b", "e", "k", "q", "t", "r", "i", "t", "n", "s"], 2, 1, 0)
#print scor_matrix
#print ""
align_matrix = p.compute_alignment_matrix(seq_x, seq_y, scor_matrix, True)
print align_matrix
score = p.compute_global_alignment(seq_x, seq_y, scor_matrix, align_matrix)
print score
#q7()
#Question 8
"""
def q7():
x = "ABCABC"
y = "ABCABC"
sm = soln.build_scoring_matrix("ABC-", 2, 1, 0)
print sm
# global
am = soln.compute_alignment_matrix(x, y, sm, True)
print soln.compute_global_alignment(x, y, sm, am)
# scoring matrix for q8
word_sm = soln.build_scoring_matrix("abcdefghijklmnopqrstuvwxyz-", 2, 1, 0)
def check_spelling(checked_word, dist, word_list):
wordlist = []
word_len = len(checked_word)
# global
for word in word_list:
am = soln.compute_alignment_matrix(checked_word, word, word_sm, True)
g_al, dummy_x, dummy_y = soln.compute_global_alignment(checked_word, word, word_sm, am)
score = word_len + len(word) - g_al
if score <= dist:
wordlist.append(word)
def test():
scoringmatrix = p.build_scoring_matrix(set(["a", "b"]), 10, 4, -6)
generate_null_distribution("aaaaaaaab", "aabbbbaabbba", scoringmatrix, 500)