def traceback(sequence1, sequence2):
alignments = []
alignmentA = ""
alignmentB = ""
i = len(sequence2) - 1
j = len(sequence1) - 1
max_number = max_number_semiglobal()
try:
j = global_alignment.matrix[len(global_alignment.matrix) -
1].index(max_number)
i = len(global_alignment.matrix) - 1
except:
j = len(global_alignment.matrix[0]) - 1
i = 0
while True:
if (global_alignment.matrix[i][j] == max_number):
break
i += 1
while (i > 0 or j > 0):
if (i > 0 and j > 0 and global_alignment.matrix[i][j]
== global_alignment.matrix[i - 1][j - 1] +
global_alignment.getScore(sequence1, sequence2, i, j)):
alignmentA = sequence1[j] + alignmentA
alignmentB = sequence2[i] + alignmentB
global_alignment.matrix[i][j] = 'D' + str(
global_alignment.matrix[i][j])
i = i - 1
j = j - 1
elif ((i > 0 and global_alignment.matrix[i][j]
== global_alignment.matrix[i - 1][j] + global_alignment.GAP)
or j == 0):
alignmentA = "--" + alignmentA
alignmentB = sequence2[i] + alignmentB
global_alignment.matrix[i][j] = "A" + str(
global_alignment.matrix[i][j])
i = i - 1
elif ((j > 0 and global_alignment.matrix[i][j]
== global_alignment.matrix[i][j - 1] + global_alignment.GAP)
or i == 0):
alignmentA = sequence1[j] + alignmentA
alignmentB = "--" + alignmentB
global_alignment.matrix[i][j] = "I" + str(
global_alignment.matrix[i][j])
j = j - 1
alignments.append(alignmentA)
alignments.append(alignmentB)
global_alignment.add_sequences(sequence1, sequence2)
return alignments
def fill_matrix(sequence1, sequence2):
sequence1 = global_alignment.insert_gap(sequence1, 0)
sequence2 = global_alignment.insert_gap(sequence2, 0)
# print(sequence1)
# print(sequence2)
num_rows = len(global_alignment.matrix)
for i in range(1,num_rows):
num_cols = len(global_alignment.matrix[i])
for j in range(1, num_cols):
up = global_alignment.matrix[i-1][j] + global_alignment.GAP
left = global_alignment.matrix[i][j-1] + global_alignment.GAP
diagonal = global_alignment.matrix[i-1][j-1] + global_alignment.getScore(sequence1, sequence2, i, j)
global_alignment.matrix[i][j] = max(up, left, diagonal, 0)
def fill_matrix(sequence1, sequence2):
sequence1 = global_alignment.insert_gap(sequence1, 0)
sequence2 = global_alignment.insert_gap(sequence2, 0)
num_rows = len(global_alignment.matrix)
#print("num_rows - " + str(num_rows))
for i in range(1, num_rows):
#print("i - " + str(i))
num_cols = len(global_alignment.matrix[i])
# print("num_cols - " + str(num_cols))
for j in range(1, num_cols):
# print("j - " + str(j))
up = global_alignment.matrix[i - 1][j] + global_alignment.GAP
# print("up done")
left = global_alignment.matrix[i][j - 1] + global_alignment.GAP
# print("left done")
diagonal = global_alignment.matrix[i - 1][
j - 1] + global_alignment.getScore(sequence1, sequence2, i, j)
# print("diagonal done")
global_alignment.matrix[i][j] = max(up, left, diagonal, 0)
def traceback(sequence1, sequence2):
alignments = []
alignmentA = ""
alignmentB = ""
argmax = np.where(
global_alignment.matrix == np.matrix(global_alignment.matrix).max())
i = argmax[0][0]
j = argmax[1][0]
while ((i > 0 or j > 0) and global_alignment.matrix[i][j] != 0):
if (i > 0 and j > 0 and global_alignment.matrix[i][j]
== global_alignment.matrix[i - 1][j - 1] +
global_alignment.getScore(sequence1, sequence2, i, j)):
alignmentA = sequence1[j] + alignmentA
alignmentB = sequence2[i] + alignmentB
global_alignment.matrix[i][j] = 'D' + str(
global_alignment.matrix[i][j]) #CAMINO
i = i - 1
j = j - 1
elif (i > 0 and global_alignment.matrix[i][j]
== global_alignment.matrix[i - 1][j] + global_alignment.GAP):
alignmentA = "--" + alignmentA
alignmentB = sequence2[i] + alignmentB
global_alignment.matrix[i][j] = "A" + str(
global_alignment.matrix[i][j]) #CAMINO
i = i - 1
else:
alignmentA = sequence1[j] + alignmentA
alignmentB = "--" + alignmentB
global_alignment.matrix[i][j] = "I" + str(
global_alignment.matrix[i][j]) #CAMINO
j = j - 1
alignments.append(alignmentA)
alignments.append(alignmentB)
global_alignment.add_sequences(sequence1, sequence2)
return alignments