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)
