Python Project4.compute_local_alignment示例

示例#1

文件： Application4_Q4.py 项目： korchynskyi/AlgorithmicThinking

def generate_null_distribution(seq_x, seq_y, scoring_matrix, num_trials):
    scoring_distribution = {}
    for i in xrange(num_trials):
        rand_y = list(seq_y)
        random.shuffle(rand_y)
        a_m = student.compute_alignment_matrix(seq_x, rand_y, scoring_matrix, False)
        alignment = student.compute_local_alignment(seq_x, rand_y, scoring_matrix, a_m)
        score = alignment[0]
        scoring_distribution[score] = scoring_distribution.get(score, 0) + 1
        print i
        #print alignment[1]
        #print alignment[2]
    return scoring_distribution

示例#2

def generate_null_distribution(seq_x, seq_y, scoring_matrix, num_trials):
    scoring_distribution = {}
    for i in xrange(num_trials):
        rand_y = list(seq_y)
        random.shuffle(rand_y)
        a_m = student.compute_alignment_matrix(seq_x, rand_y, scoring_matrix,
                                               False)
        alignment = student.compute_local_alignment(seq_x, rand_y,
                                                    scoring_matrix, a_m)
        score = alignment[0]
        scoring_distribution[score] = scoring_distribution.get(score, 0) + 1
        print i
        #print alignment[1]
        #print alignment[2]
    return scoring_distribution