def generate_null_distribution(seq_x,seq_y, scoring_matrix, num_trials):
retdic = {}
#cnt = 0
while num_trials > 0:
#seq_y = random.shuffle(seq_y)
#seq_y = ''.join(random.sample(seq_y,len(seq_y)))
l = list(seq_y)
random.shuffle(l)
seq_y = ''.join(l)
alignment_matrix = PR.compute_alignment_matrix(seq_x, seq_y, scoring_matrix, False)
#print alignment_matrix
res = PR.compute_local_alignment(seq_x, seq_y, scoring_matrix, alignment_matrix)
#calc MAX
'''vals = []
for fst in alignment_matrix:
vals.append(max(fst))
ith = vals.index(max(vals))
jth = alignment_matrix[ith].index(max(alignment_matrix[ith])) '''
#print "ALI = ", alignment_matrix[ith][jth]
#print "res = ", res[0]
#print "------------"
#ali0 = alignment_matrix[ith][jth] #~!!!!!!!!!!!!!!!!!!!!!!!!!!
#print "score = ", res[0]
if retdic.has_key(res[0]):
temp = retdic[res[0]]
retdic[res[0]] = temp+1
else:
retdic[res[0]] = 1
#cnt += 1
num_trials -= 1
return retdic
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
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)
# humanEyelessProtein = "http://storage.googleapis.com/codeskulptor-alg/alg_HumanEyelessProtein.txt"
# fruitflyEyelessProtein = "http://storage.googleapis.com/codeskulptor-alg/alg_FruitflyEyelessProtein.txt"
# scoringMatrixPAM50 = "http://storage.googleapis.com/codeskulptor-alg/alg_PAM50.txt"
pro1 = LoadHelper.read_protein(LoadHelper.HUMAN_EYELESS_URL)
pro2 = LoadHelper.read_protein(LoadHelper.FRUITFLY_EYELESS_URL)
matr = LoadHelper.read_scoring_matrix(LoadHelper.PAM50_URL)
cpax = LoadHelper.read_protein(LoadHelper.CONSENSUS_PAX_URL)
localHum = "HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVSKIAQYKRECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLASEK-QQ"
localHum_dashless = "HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVSKIAQYKRECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLASEKQQ"
localFly = "HSGVNQLGGVFVGGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATAEVVSKISQYKRECPSIFAWEIRDRLLQENVCTNDNIPSVSSINRVLRNLAAQKEQQ"
alimat = PR.compute_alignment_matrix(localFly, cpax, matr, True)
a1 = PR.compute_global_alignment(localFly, cpax, matr, alimat)
print a1
# s1 = ''.join(random.choice("ACBEDGFIHKMLNQPSRTWVYXZ") for x in range(130))
# s2 = ''.join(random.choice("ACBEDGFIHKMLNQPSRTWVYXZ") for x in range(130))
# a1 = (12, s1, s2)
cnt = 0
for ith, jth in zip(a1[1], a1[2]):
if ith == jth:
cnt += 1
print cnt / (len(a1[1]) * 1.0)
import Project as PR
import string
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)
