def needle(seq1, seq2):
m, n = len(seq1), len(seq2) # length of two sequences
# Generate DP table and traceback path pointer matrix
score = align.zeros((m + 1, n + 1)) # the DP table
# Calculate DP table
for i in range(0, m + 1):
score[i][0] = align.gap_penalty * i
for j in range(0, n + 1):
score[0][j] = align.gap_penalty * j
for i in range(1, m + 1):
for j in range(1, n + 1):
match = score[i - 1][j - 1] + align.match_score(seq1[i - 1], seq2[j - 1])
delete = score[i - 1][j] + align.gap_penalty
insert = score[i][j - 1] + align.gap_penalty
score[i][j] = max(match, delete, insert)
# Traceback and compute the alignment
align1, align2 = '', ''
i, j = m, n # start from the bottom right cell
while i > 0 and j > 0: # end touching the top or the left edge
score_current = score[i][j]
score_diagonal = score[i - 1][j - 1]
score_up = score[i][j - 1]
score_left = score[i - 1][j]
if score_current == score_diagonal + align.match_score(seq1[i - 1], seq2[j - 1]):
align1 += seq1[i - 1]
align2 += seq2[j - 1]
i -= 1
j -= 1
elif score_current == score_left + align.gap_penalty:
align1 += seq1[i - 1]
align2 += '-'
i -= 1
elif score_current == score_up + align.gap_penalty:
align1 += '-'
align2 += seq2[j - 1]
j -= 1
# Finish tracing up to the top left cell
while i > 0:
align1 += seq1[i - 1]
align2 += '-'
i -= 1
while j > 0:
align1 += '-'
align2 += seq2[j - 1]
j -= 1
align.finalize(align1, align2)
def water(seq1, seq2):
m, n = len(seq1), len(seq2) # length of two sequences
# Generate DP table and traceback path pointer matrix
score = align.zeros((m + 1, n + 1)) # the DP table
pointer = align.zeros((m + 1, n + 1)) # to store the traceback path
max_i, max_j = 0, 0
max_score = 0 # 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_diagonal = score[i - 1][j - 1] + align.match_score(seq1[i - 1], seq2[j - 1])
score_up = score[i][j - 1] + align.gap_penalty
score_left = score[i - 1][j] + align.gap_penalty
score[i][j] = max(0, score_left, score_up, score_diagonal)
if score[i][j] == 0:
pointer[i][j] = 0 # 0 means end of the path
if score[i][j] == score_left:
pointer[i][j] = 1 # 1 means trace up
if score[i][j] == score_up:
pointer[i][j] = 2 # 2 means trace left
if score[i][j] == score_diagonal:
pointer[i][j] = 3 # 3 means trace diagonal
if score[i][j] >= max_score:
max_i = i
max_j = j
max_score = score[i][j]
align1, align2 = '', '' # initial sequences
i, j = max_i, max_j # indices of path starting point
# traceback, follow pointers
while pointer[i][j] != 0:
if pointer[i][j] == 3:
align1 += seq1[i - 1]
align2 += seq2[j - 1]
i -= 1
j -= 1
elif pointer[i][j] == 2:
align1 += '-'
align2 += seq2[j - 1]
j -= 1
elif pointer[i][j] == 1:
align1 += seq1[i - 1]
align2 += '-'
i -= 1
align.finalize(align1, align2)
def needleman_wunsch(seq1, seq2):
try:
m, n = len(seq1), len(seq2)
score = align.zeros((m + 1, n + 1))
# Create the table
for i in range(0, m + 1):
score[i][0] = align.gap_penalty * i
for j in range(0, n + 1):
score[0][j] = align.gap_penalty * j
for i in range(1, m + 1):
for j in range(1, n + 1):
match = score[i - 1][j - 1] + align.match_score(seq1[i - 1], seq2[j - 1])
delete = score[i - 1][j] + align.gap_penalty
insert = score[i][j - 1] + align.gap_penalty
score[i][j] = max(match, delete, insert)
align1, align2 = "", ""
i, j = m, n
while i > 0 and j > 0:
score_current = score[i][j]
score_diagonal = score[i - 1][j - 1]
score_up = score[i][j - 1]
score_left = score[i - 1][j]
if score_current == score_diagonal + align.match_score(seq1[i - 1], seq2[j - 1]):
align1 += seq1[i - 1]
align2 += seq2[j - 1]
i -= 1
j -= 1
elif score_current == score_left + align.gap_penalty:
align1 += seq1[i - 1]
align2 += "-"
i -= 1
elif score_current == score_up + align.gap_penalty:
align1 += "-"
align2 += seq2[j - 1]
j -= 1
# Back tracking
while i > 0:
align1 += seq1[i - 1]
align2 += "-"
i -= 1
while j > 0:
align1 += "-"
align2 += seq2[j - 1]
j -= 1
return align.finalize(align1, align2)
except Exception as exp:
# log.error("Can not align the sequences", exp)
print exp
