newalign_y = ""
trail = True
for ith, jth in zip(align_x, align_y):
if (ith or jth) == "-" and trail == True:
trail = True
else:
newalign_x += ith
newalign_y += jth
trail = False '''
oldscore = score
score = 0
for ith, jth in zip(align_x, align_y):
score += scoring_matrix[ith][jth]
#score = alignment_matrix[len(seq_x)][len(seq_y)]
print "Oldscore = ", oldscore
print "VALIDANCE = ", oldscore == score
return (score, align_x, align_y)
pro1 = LoadHelper.read_protein(LoadHelper.HUMAN_EYELESS_URL)
pro2 = LoadHelper.read_protein(LoadHelper.FRUITFLY_EYELESS_URL)
matr = LoadHelper.read_scoring_matrix(LoadHelper.PAM50_URL)
alimat = PR.compute_alignment_matrix(pro1, pro2, matr, False)
print compute_local_alignment(pro1, pro2, matr, alimat)
import LoadHelper
str1 = "sadness"
str2 = "straw"
#str1 = "kitten"
#str2 = "sitting"
alphabet = list(string.ascii_lowercase)
matrix = PR.build_scoring_matrix(alphabet, 2 ,1, 0)
alig = PR.compute_alignment_matrix(str1, str2, matrix, True)
res = PR.compute_global_alignment(str1, str2, matrix, alig)
#print res
#print "EDIT dist = ", len(str1)+len(str2)-res[0]
word_list = LoadHelper.read_words(LoadHelper.WORD_LIST_URL)
#print "WL = ", word_list
def check_spelling(checked_word, dist, word_list):
matrix = PR.build_scoring_matrix(alphabet, 2 ,1, 0)
retlist = []
str1 = checked_word
for ith in word_list:
str2 = ith
alig = PR.compute_alignment_matrix(str1, str2, matrix, True)
res = PR.compute_global_alignment(str1, str2, matrix, alig)
edit_dist = len(str1)+len(str2)-res[0]
if edit_dist <= dist:
retlist.append(str2)
return retlist
