def get_orientation(self, si, sj):
"""
si, sj are two number series. To compute whether these two series have
same orientation or not. We combine them in the two orientation
configurations and compute length of the longest monotonic series.
"""
if not si or not sj:
return 0
# Same orientation configuration
a = lms(si + sj)
b = lms(sj + si)
# Opposite orientation configuration
c = lms(si + sj[::-1])
d = lms(sj[::-1] + si)
return max(a, b)[0] - max(c, d)[0]
def get_orientation(self, si, sj):
"""
si, sj are two number series. To compute whether these two series have
same orientation or not. We combine them in the two orientation
configurations and compute length of the longest monotonic series.
"""
if not si or not sj:
return 0
# Same orientation configuration
a = lms(si + sj)
b = lms(sj + si)
# Opposite orientation configuration
c = lms(si + sj[::-1])
d = lms(sj[::-1] + si)
return max(a, b)[0] - max(c, d)[0]
def colinear_evaluate_multi(tour, scfs, weights):
weighted_score = 0
for scf, w in zip(scfs, weights):
subtour = [x for x in tour if x in scf]
series = []
for t in subtour:
series.extend(scf[t])
score, diff = lms(series)
weighted_score += score * w
return (weighted_score, )
def colinear_evaluate_multi(tour, scfs, weights):
weighted_score = 0
for scf, w in zip(scfs, weights):
subtour = [x for x in tour if x in scf]
series = []
for t in subtour:
series.extend(scf[t])
score, diff = lms(series)
weighted_score += score * w
return (weighted_score,)
def fix_orientation(self, tour):
"""
Test each scaffold if flipping will increass longest monotonic chain
length.
"""
orientations = dict(tour) # old configuration here
scaffold_oo = defaultdict(list)
scaffolds, oos = zip(*tour)
for mlg in self.linkage_groups:
lg = mlg.lg
mapname = mlg.mapname
for s, o in tour:
i = scaffolds.index(s)
L = [self.get_series(lg, x, xo) for x, xo in tour[:i]]
U = [self.get_series(lg, x, xo) for x, xo in tour[i + 1:]]
L, U = list(flatten(L)), list(flatten(U))
M = self.get_series(lg, s)
plus = lms(L + M + U)
minus = lms(L + M[::-1] + U)
d = plus[0] - minus[0]
if not d:
continue
scaffold_oo[s].append((d, mapname)) # reset orientation
fixed = 0
for s, v in scaffold_oo.items():
d = self.weighted_mean(v)
old_d = orientations[s]
new_d = np.sign(d)
if new_d != old_d:
orientations[s] = new_d
fixed += 1
tour = [(x, orientations[x]) for x in scaffolds]
logging.debug("Fixed orientations for {0} scaffolds.".format(fixed))
return tour
def fix_orientation(self, tour):
"""
Test each scaffold if flipping will increass longest monotonic chain
length.
"""
orientations = dict(tour) # old configuration here
scaffold_oo = defaultdict(list)
scaffolds, oos = zip(*tour)
for mlg in self.linkage_groups:
lg = mlg.lg
mapname = mlg.mapname
for s, o in tour:
i = scaffolds.index(s)
L = [self.get_series(lg, x, xo) for x, xo in tour[:i]]
U = [self.get_series(lg, x, xo) for x, xo in tour[i + 1:]]
L, U = list(flatten(L)), list(flatten(U))
M = self.get_series(lg, s)
plus = lms(L + M + U)
minus = lms(L + M[::-1] + U)
d = plus[0] - minus[0]
if not d:
continue
scaffold_oo[s].append((d, mapname)) # reset orientation
fixed = 0
for s, v in scaffold_oo.items():
d = self.weighted_mean(v)
old_d = orientations[s]
new_d = np.sign(d)
if new_d != old_d:
orientations[s] = new_d
fixed += 1
tour = [(x, orientations[x]) for x in scaffolds]
logging.debug("Fixed orientations for {0} scaffolds.".format(fixed))
return tour