def construct_alignment(l, c, trace, s1, s2, op):
current = (l, c)
path = ["", ""]
deletedpath = False
while current != (0, 0):
all_previous = trace[current]
previous = all_previous[0]
direction = all_previous[0][1]
if len(all_previous) > 1:
op += 1
if not deletedpath:
del trace[current][0]
deletedpath = True
if direction == "diag":
path[0] += s1[current[1] - 1]
path[1] += s2[current[0] - 1]
elif direction == "down":
path[0] += "-"
path[1] += s2[current[0] - 1]
elif direction == "right":
path[0] += s1[current[1] - 1]
path[1] += "-"
else:
#free taxi ride
pass
current = previous[0]
distance = hamming_d(path[0], path[1])
return [path[0][::-1], path[1][::-1], distance], op
def construct_alignment(l, c, trace, s1, s2, op):
current = (l, c)
path = ["", ""]
deletedpath = False
while current != (0, 0):
all_previous = trace[current]
previous = all_previous[0]
direction = all_previous[0][1]
if len(all_previous) > 1:
op += 1
if not deletedpath:
del trace[current][0]
deletedpath = True
if direction == "diag":
path[0] += s1[current[1] - 1]
path[1] += s2[current[0] - 1]
elif direction == "down":
path[0] += "-"
path[1] += s2[current[0] - 1]
elif direction == "right":
path[0] += s1[current[1] - 1]
path[1] += "-"
else:
#free taxi ride
pass
current = previous[0]
distance = hamming_d(path[0], path[1])
return [path[0][::-1], path[1][::-1], distance], op
def distance(pattern, dna):
k = len(pattern)
d = 0
for s in dna:
hd = k
for i in range(len(s) - k):
p = s[i:i + k]
nhd = hamming_d(pattern, p)
if nhd < hd:
hd = nhd
d += hd
return d
def distance(pattern, dna):
k = len(pattern)
d = 0
for s in dna:
hd = k
for i in range(len(s) - k):
p = s[i:i + k]
nhd = hamming_d(pattern, p)
if nhd < hd:
hd = nhd
d += hd
return d
def construct_alignment_all(start, trace, s1, s2, op, choice_track, retrack):
should_retrack = False
if len(choice_track) > 0:
path = choice_track[-1][0]
current = choice_track[-1][1]
retrack.append((current, trace[(current, 0)][0]))
del trace[(current, 0)][0]
if len(trace[current]) == 1:
del choice_track[-1]
should_retrack = True
else:
current = start
path = ["", ""]
while current[0] != (0, 0):
all_previous = trace[current]
previous = all_previous[0]
# direction = all_previous[0][1]
atual = current[1]
if len(all_previous) > 1:
op += 1
choice_track.append([path[:], current])
#middle matrix is diagonal
if atual == 0:
path[0] += s1[current[0][1] - 1]
path[1] += s2[current[0][0] - 1]
#lower matrix is down
elif atual == -1:
path[0] += "-"
path[1] += s2[current[0][0] - 1]
#upper matrix is right
elif atual == 1:
path[0] += s1[current[0][1] - 1]
path[1] += "-"
else:
#free taxi ride
pass
current = previous
if should_retrack:
for r in retrack[:]:
trace.setdefault(r[0], []).append(r[1])
retrack.remove(r)
distance = hamming_d(path[0], path[1])
return [path[0][::-1], path[1][::-1], distance], op
def construct_alignment_all(start, trace, s1, s2, op, choice_track, retrack):
should_retrack = False
if len(choice_track) > 0:
path = choice_track[-1][0]
current = choice_track[-1][1]
retrack.append((current, trace[(current, 0)][0]))
del trace[(current, 0)][0]
if len(trace[current]) == 1:
del choice_track[-1]
should_retrack = True
else:
current = start
path = ["", ""]
while current[0] != (0, 0):
all_previous = trace[current]
previous = all_previous[0]
# direction = all_previous[0][1]
atual = current[1]
if len(all_previous) > 1:
op += 1
choice_track.append([path[:], current])
#middle matrix is diagonal
if atual == 0:
path[0] += s1[current[0][1] - 1]
path[1] += s2[current[0][0] - 1]
#lower matrix is down
elif atual == -1:
path[0] += "-"
path[1] += s2[current[0][0] - 1]
#upper matrix is right
elif atual == 1:
path[0] += s1[current[0][1] - 1]
path[1] += "-"
else:
#free taxi ride
pass
current = previous
if should_retrack:
for r in retrack[:]:
trace.setdefault(r[0], []).append(r[1])
retrack.remove(r)
distance = hamming_d(path[0], path[1])
return [path[0][::-1], path[1][::-1], distance], op
def construct_alignment_all(l, c, trace, s1, s2, op, choice_track, retrack):
should_retrack = False
if len(choice_track) > 0:
path = choice_track[-1][0]
current = choice_track[-1][1]
retrack.append((current, trace[current][0]))
del trace[current][0]
if len(trace[current]) == 1:
del choice_track[-1]
should_retrack = True
else:
current = (l, c)
path = ["", ""]
while current != (0, 0):
all_previous = trace[current]
previous = all_previous[0]
direction = all_previous[0][1]
if len(all_previous) > 1:
op += 1
choice_track.append([path[:], current])
if direction == "diag":
path[0] += s1[current[1] - 1]
path[1] += s2[current[0] - 1]
elif direction == "down":
path[0] += "-"
path[1] += s2[current[0] - 1]
elif direction == "right":
path[0] += s1[current[1] - 1]
path[1] += "-"
else:
#free taxi ride
pass
current = previous[0]
if should_retrack:
for r in retrack[:]:
trace.setdefault(r[0], []).append(r[1])
retrack.remove(r)
distance = hamming_d(path[0], path[1])
return [path[0][::-1], path[1][::-1], distance], op
def construct_alignment_all(l, c, trace, s1, s2, op, choice_track, retrack):
should_retrack = False
if len(choice_track) > 0:
path = choice_track[-1][0]
current = choice_track[-1][1]
retrack.append((current, trace[current][0]))
del trace[current][0]
if len(trace[current]) == 1:
del choice_track[-1]
should_retrack = True
else:
current = (l, c)
path = ["", ""]
while current != (0, 0):
all_previous = trace[current]
previous = all_previous[0]
direction = all_previous[0][1]
if len(all_previous) > 1:
op += 1
choice_track.append([path[:], current])
if direction == "diag":
path[0] += s1[current[1] - 1]
path[1] += s2[current[0] - 1]
elif direction == "down":
path[0] += "-"
path[1] += s2[current[0] - 1]
elif direction == "right":
path[0] += s1[current[1] - 1]
path[1] += "-"
else:
#free taxi ride
pass
current = previous[0]
if should_retrack:
for r in retrack[:]:
trace.setdefault(r[0], []).append(r[1])
retrack.remove(r)
distance = hamming_d(path[0], path[1])
return [path[0][::-1], path[1][::-1], distance], op
def score_real_motif(mots, cons):
count = 0.0
for m in mots:
count += hamming_d(m, cons)
return count
def score_real_motif(mots, cons):
count = 0.0
for m in mots:
count += hamming_d(m, cons)
return count