def __ddEvent(self):
if self.pool.size() == 0 or self.pool.weight() == 1:
return
sampleNode1, offset1, sampleNode2, offset2 = self.__drawSamples()
c1 = sampleNode1.data
c2 = sampleNode2.data
# only deal with dead / dead contigs in this event
if (c1.isDead() == False or c2.isDead() == False):
return
# only support single dead contig
assert c1 is c2
# don't know what to do here
if (offset1 == offset2):
return
self.pool.remove(sampleNode1)
if c1 is not c2:
self.pool.remove(sampleNode2)
#forward means do not cut
forward = random.random() > self.pgain
# do the dcj
dcjResult = dcj(c1, offset1, c2, offset2, forward)
deadIdx = 0;
if len(dcjResult) == 2 and \
random.randint(0, dcjResult[0].size + dcjResult[1].size) \
>= dcjResult[0].size:
deadIdx = 1
dcjResult[deadIdx].setDead(True)
if forward:
self.ddSwapCount += 1
assert len(dcjResult) == 1
else:
self.ddGainCount += 1
assert len(dcjResult) == 2
assert not dcjResult[0].isDead() or not dcjResult[1].isDead()
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
def __ldEvent(self):
if self.pool.size() == 0 or self.pool.weight() == 1:
return
# draw (and remove) two random adajcenies and their
#contigs from the pool (only if they are not dead)
sampleNode1, offset1, sampleNode2, offset2 = self.__drawSamples()
c1 = sampleNode1.data
c2 = sampleNode2.data
# only deal with live / dead contigs in this event
if (c1.isDead() == c2.isDead()):
return
self.pool.remove(sampleNode1)
if c1 is not c2:
self.pool.remove(sampleNode2)
# make sure c1 is alive and c2 is dead
if c1.isDead():
c1, c2 = c2, c1
offset1, offset2 = offset2, offset1
# do the dcj
dcjResult = dcj(c1, offset1, c2, offset2, random.randint(0, 1) == 1)
deadIdx = 0;
if len(dcjResult) == 2 and \
random.randint(0, dcjResult[0].size + dcjResult[1].size) >= \
dcjResult[0].size:
deadIdx = 1
dcjResult[deadIdx].setDead(True)
if len(dcjResult) == 1:
self.ldLossCount += 1
else:
self.ldSwapCount += 1
# add the resulting contigs back to the pool
deadCount = 0
for res in dcjResult:
if res.isDead():
deadCount += 1
self.pool.insert(res, res.numBases())
assert deadCount == 1
def __llGain(self, c1, c2, offset1, offset2):
# correct "not composite check below"
if c1.isCircular() or (offset1 != 0 and offset1 != c1.size - 1):
forward = self.fg > random.random()
if forward:
self.fgCount += 1
dcjResult = dcj(c1, offset1, c2, offset2, forward)
if c1.isCircular():
assert len(dcjResult) == 1 and dcjResult[0].isLinear()
else:
assert len(dcjResult) == 2 and dcjResult[0].isLinear() \
and dcjResult[1].isLinear()
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
return
self.pool.insert(c1, c1.numBases())
if c2 is not c1:
self.pool.insert(c2, c2.numBases())
def __llEvent(self):
if self.pool.size() == 0 or self.pool.weight() == 1:
return
# draw (and remove) two random adajcenies and their
#contigs from the pool (only if they are not dead)
sampleNode1, offset1, sampleNode2, offset2 = self.__drawSamples()
c1 = sampleNode1.data
c2 = sampleNode2.data
# don't deal with dead contigs in this event
if c1.isDead() == True or c2.isDead() == True:
return
self.pool.remove(sampleNode1)
if c1 is not c2:
self.pool.remove(sampleNode2)
# case 1) gain of telomere
if sampleNode1 is sampleNode2 and offset1 == offset2:
return self.__llGain(c1, c2, offset1, offset2)
# case 2) loss of telomere
elif c1.isLinear() and c2.isLinear() and \
(offset1 == 0 or offset1 == c1.size - 1) and \
(offset2 == 0 or offset2 == c2.size - 1):
return self.__llLoss(c1, c2, offset1, offset2)
# case 3) no gain or loss
self.llCount += 1
forward = random.randint(0, 1) == 1
# do the dcj
dcjResult = dcj(c1, offset1, c2, offset2, forward)
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
def __llLoss(self, c1, c2, offset1, offset2):
if c1 is c2:
forward = self.fl / 4.0 > random.random()
else:
forward = self.fl / 2.0 > random.random()
if forward:
c1 = c1.circularize()
if c1 is not c2:
c2 = c2.circularize()
dcjResult = dcj(c1, offset1, c2, offset2, forward)
self.flCount += 1
assert len(dcjResult) == 1
if c1 is not c2:
assert dcjResult[0].isLinear()
else:
assert dcjResult[0].isCircular()
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
else:
self.pool.insert(c1, c1.numBases())
if c2 is not c1:
self.pool.insert(c2, c2.numBases())
