def needleman_wunsch_matrix(self,seq1, seq2):
"""
fill in the DP matrix according to the Needleman-Wunsch algorithm.
Returns the matrix of scores and the matrix of pointers
"""
indel = -1 # indel penalty
n = len(seq1)
m = len(seq2)
s = np.zeros( (n+1, m+1) ) # DP matrix
ptr = np.zeros( (n+1, m+1), dtype=int ) # matrix of pointers
##### INITIALIZE SCORING MATRIX (base case) #####
for i in range(1, n+1) :
s[i,0] = indel * i
for j in range(1, m+1):
s[0,j] = indel * j
########## INITIALIZE TRACEBACK MATRIX ##########
# Tag first row by LEFT, indicating initial "-"s
ptr[0,1:] = self.LEFT
# Tag first column by UP, indicating initial "-"s
ptr[1:,0] = self.UP
#####################################################
for i in range(1,n+1):
for j in range(1,m+1):
# match
simpleAlign=Alignment()
simpleAlign.needleman_wunsch(seq1[i-1], seq2[j-1])
score=simpleAlign.score
s[i,j] = s[i-1,j-1]+ score
# indel penalty
if s[i-1,j] + indel > s[i,j] :
s[i,j] = s[i-1,j] + indel
ptr[i,j] = self.UP
# indel penalty
if s[i, j-1] + indel > s[i,j]:
s[i,j] = s[i, j-1] + indel
ptr[i,j] = self.LEFT
return s, ptr
def needleman_wunsch_matrix(self, seq1, seq2):
"""
fill in the DP matrix according to the Needleman-Wunsch algorithm.
Returns the matrix of scores and the matrix of pointers
"""
indel = -1 # indel penalty
n = len(seq1)
m = len(seq2)
s = np.zeros((n + 1, m + 1)) # DP matrix
ptr = np.zeros((n + 1, m + 1), dtype=int) # matrix of pointers
##### INITIALIZE SCORING MATRIX (base case) #####
for i in range(1, n + 1):
s[i, 0] = indel * i
for j in range(1, m + 1):
s[0, j] = indel * j
########## INITIALIZE TRACEBACK MATRIX ##########
# Tag first row by LEFT, indicating initial "-"s
ptr[0, 1:] = self.LEFT
# Tag first column by UP, indicating initial "-"s
ptr[1:, 0] = self.UP
#####################################################
for i in range(1, n + 1):
for j in range(1, m + 1):
# match
simpleAlign = Alignment()
simpleAlign.needleman_wunsch(seq1[i - 1], seq2[j - 1])
score = simpleAlign.score
s[i, j] = s[i - 1, j - 1] + score
# indel penalty
if s[i - 1, j] + indel > s[i, j]:
s[i, j] = s[i - 1, j] + indel
ptr[i, j] = self.UP
# indel penalty
if s[i, j - 1] + indel > s[i, j]:
s[i, j] = s[i, j - 1] + indel
ptr[i, j] = self.LEFT
return s, ptr
