BLAST-用python实现

最近在自学python，又用python实现了一下BLAST。

这次更新了打分函数如下，空位罚分改为-5，但不区分gap open 和 gap extend。

	A	G	C	T
A	2	-7	-5	-7
G	-7	2	-7	-5
C	-5	-7	2	-7
T	-7	-5	-7	2

'''
@author: JiuYu
'''

def score(a,b):#scoring function
    score=0
    lst=['AC','GT','CA','TG']
    if a==b:
        score +=2
    elif a+b in lst:
        score += -5
    else:
        score += -7
    return score

def BLAST(seq1,seq2):#Basic Local Alignment Search Tool
    l1 = len(seq1)
    l2 = len(seq2)
    GAP =-5     #-5 for any gap
    scores =[]
    point =[]
    
    for j in range(l2+1):
        if j == 0:
            line1=[0]
            line2=[0]
            for i in range(1,l1+1):
                line1.append(GAP*i)
                line2.append(2)
        else:
            line1=[]
            line2=[]
            line1.append(GAP*j)
            line2.append(3)
        scores.append(line1)
        point.append(line2)
    
    #fill the blank of scores and point
    for j in range(1,l2+1):
        letter2 = seq2[j-1]
        for i in range(1,l1+1):
            letter1 = seq1[i-1]
            diagonal_score = score(letter1, letter2) + scores[j-1][i-1]
            left_score = GAP + scores[j][i-1]
            up_score = GAP + scores[j-1][i]
            max_score = max(diagonal_score, left_score, up_score)
            scores[j].append(max_score)
            
            if scores[j][i] == diagonal_score:
                point[j].append(1)
            elif scores[j][i] == left_score:
                point[j].append(2)
            else:
                point[j].append(3)
                
    #trace back
    alignment1=''
    alignment2=''
    i = l2
    j = l1
    print 'scores =',scores[i][j]
    while True:
        if point[i][j] == 0:
            break
        elif point[i][j] == 1:
            alignment1 += seq1[j-1]
            alignment2 += seq2[i-1]
            i -= 1
            j -= 1
        elif point[i][j] == 2:
            alignment1 += seq1[j-1]
            alignment2 += '-'
            j -= 1
        else:
            alignment1 += '-'
            alignment2 += seq2[i-1]
            i -= 1
            
    #reverse alignment
    alignment1 = alignment1[::-1]
    alignment2 = alignment2[::-1]
    print 'The best alignment:'
    print alignment1
    print alignment2

seq1=raw_input('Please input your first sequences:\n')
seq2=raw_input('input second sequences:\n')
BLAST(seq1, seq2)

运行结果：

无疑python对字符串的处理更加强大，语言也更加简单，优雅。比如最后逆序输出alignment，java我是单独写了一个逆序函数，而python只用一个语句就可以完成相同任务。