Python Project.compute_global_alignment Examples

Example #1

File: Q7.py Project: Uhha/Assignment2

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

Example #2

File: Q2.py Project: Uhha/Assignment2

# 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)

Example #3

File: Q7.py Project: Uhha/Assignment2

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)