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 Project as PR import LoadHelper import random import string # 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