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Genomics/SmithWaterman2.py
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#This software is a free software. Thus, it is licensed under GNU General Public License version 3 or later. | |
#Python implementation to Smith-Waterman Algorithm for Homework 1 of Bioinformatics class. | |
#Forrest Bao, Sept. 26, 2007 <http://fsbao.net> <forrest.bao aT gmail.com> | |
from random import * | |
alpha='cagt' | |
#read the first sequence | |
seq1='' | |
seq2='' | |
for i in range(6): | |
seq1=seq1+choice(alpha); | |
for i in range(15): | |
seq2=seq2+choice(alpha); | |
seq1='gggggg' | |
seq2='ggctttggtcacg' | |
print seq1, "\n", seq2 | |
m,n = len(seq1),len(seq2) #length of two sequences | |
#generate DP table and traceback path pointer matrix | |
score=[[float(0) for j in range(n+1)] for i in range(m+1)] | |
pointer=[[float(0) for j in range(n+1)] for i in range(m+1)] | |
P=0; | |
penalty=0 | |
def match_score(alpha,beta): | |
if alpha==beta: | |
return 10 | |
else: | |
return -8 | |
max_score=P; #initial maximum score in DP table | |
#calculate DP table and mark pointers | |
for i in range(1,m+1): | |
for j in range(1,n+1): | |
score_up=score[i-1][j]+penalty | |
score_down=score[i][j-1]+penalty | |
score_diagonal=score[i-1][j-1]+match_score(seq1[i-1],seq2[j-1]); | |
score[i][j]=max(0.0,score_up,score_down,score_diagonal); | |
if score[i][j]==0: | |
pointer[i][j]=0; #0 means end of the path | |
if score[i][j]==score_up: | |
pointer[i][j]=1; #1 means trace up | |
if score[i][j]==score_down: | |
pointer[i][j]=2; #2 means trace left | |
if score[i][j]==score_diagonal: | |
print i,j, score[i][j] | |
pointer[i][j]=3; #3 means trace diagonal | |
if score[i][j]>=max_score: | |
print i,j,score[i][j],max_score | |
max_i=i; | |
max_j=j; | |
max_score=score[i][j]; | |
#END of DP table | |
for i in range(m+1): | |
for j in range(n+1): | |
print '{0:2f}'.format(score[i][j]), '{0:2d}'.format(int(pointer[i][j])), '|', | |
align1,align2='',''; #initial sequences | |
i,j=max_i,max_j; | |
print "Found:", max_i, max_j, score[i][j], pointer[i][j] | |
#indices of path starting point | |
#missing beginning and ending for this routine | |
#traceback, follow pointers | |
while pointer[i][j]!=0: | |
if pointer[i][j]==3: | |
align1=align1+seq1[i-1]; | |
align2=align2+seq2[j-1]; | |
i=i-1; | |
j=j-1; | |
elif pointer[i][j]==2: | |
align1=align1+'-'; | |
align2=align2+seq2[j-1]; | |
j=j-1; | |
elif pointer[i][j]==1: | |
align1=align1+seq1[i-1]; | |
align2=align2+'-'; | |
i=i-1; | |
#END of traceback | |
align1=align1[::-1]; #reverse sequence 1 | |
align2=align2[::-1]; #reverse sequence 2 | |
i,j=0,0; | |
#calcuate identity, similarity, score and aligned sequeces | |
def result(align1,align2): | |
symbol=''; | |
score=0; | |
identity,similarity=0,0; | |
for i in range(0,len(align1)): | |
if align1[i]==align2[i]: #if two AAs are the same, then output the letter | |
symbol=symbol+align1[i]; | |
identity=identity+1; | |
score=score+match_score(align1[i],align2[i]); | |
elif align1[i]=='-' or align2[i]=='-': #if one of them is a gap, output a space | |
symbol=symbol+' '; | |
score=score+penalty | |
print 'length of common subsequence = ', identity | |
print 'Score =', score; | |
print align1 | |
print align2 | |
print symbol | |
#END of function result | |
result(align1,align2) |