def testTrees():
a = ArtificialPhylogeny(size=20,numChromosomes=5)
while len(a.tree.getTips()) < 6:
a.evolve()
tipScores = [tip.getScore() for tip in a.tree.getTips()]
s = a.tree.getScore()
tipScores = [score -s for score in tipScores]
for score in tipScores:
assert score == 0
copyTree = Tree(a.tree)
if len(a.tree) != len(copyTree):
print( len(a.tree) )
print( len(copyTree))
print( a.tree.getTips())
print(copyTree.getTips())
print(a.tree)
print(copyTree)
print(a.tree.genome.getName())
print(copyTree.genome.getName())
raise Exception("Trees are not the same size")
sub = a.tree.subs[0]
a.tree.breakConnection( sub )
if len(copyTree.subs) not in (1,3):
print( len(copyTree.subs))
assert False
a.tree.addConnection( sub)
aTips = a.tree.getTips()
for cTip in copyTree.getTips():
assert cTip not in aTips
tipScores = [tip.getScore() for tip in a.tree.getTips()]
s = a.tree.getScore()
tipScores = [score -s for score in tipScores]
for score in tipScores:
assert score == 0
aTips = a.tree.getTips()
subTips = a.tree.subs[0].getTips()
for tip in aTips:
assert tip in subTips
assert 2*len(copyTree.getTips()) - 2 == len(copyTree)
print("All tree tests passed.")
class ArtificialPhylogeny( object ): def __init__( self, size=5, numChromosomes=3): self.original = Genome(name="origin") for c in range( numChromosomes ): self.original.addChromosome(range( c*size+1, (c+1)*size+1 )) self.firstRound = True self.tree = Tree( self.original ) def mutate(self, ancestor): mod = rn.choice( ["REVERSAL", "TRANSLOCATION"] ) def reversal( ancestor ): n = ancestor.getName() chromosome = rn.choice(ancestor.chromosomeList) if len(chromosome) == 0: print(ancestor) assert False start = rn.randrange(len(chromosome)) end = rn.randrange( start, min(len(chromosome), 1 + start + len(chromosome)/10) ) a,b,c = chromosome[:start], chromosome[start:end:], chromosome[end:] b = [-1*val for val in b] b = b[::-1] revChromosome = a + b + c assert len(revChromosome) == len(chromosome) ind = ancestor.chromosomeList.index(chromosome) ancestor.chromosomeList[ind] = revChromosome def translocate( ancestor ): n = ancestor.getName() (chrA, chrB) = rn.sample(ancestor.chromosomeList,2) stA,stB = rn.randint(0, len(chrA)), rn.randint(0, len(chrB)) enA = rn.randint(stA, min(len(chrA), 1 + stA + len(chrA)/10)) enB = rn.randint(stB, min(len(chrB), 1 + stB + len(chrB)/10)) transA= [a for i, a in enumerate(chrA) if i >= stA and i <=enA] if rn.random() < 0.5: transA = transA[::-1] transA = [-val for val in transA] transB= [b for i, b in enumerate(chrB) if i >= stB and i <=enB] if rn.random() < 0.5: transB = transB[::-1] transB = [-val for val in transB] frontA, backA, frontB, backB = chrA[:stA], chrA[enA+1:], chrB[:stB], chrB[enB+1:] tempA, tempB = frontA+transB+backA, frontB+transA+backB aInd = ancestor.chromosomeList.index(chrA) if len(tempA) > 0: ancestor.chromosomeList[aInd] = tempA else: ancestor.chromosomeList.pop(aInd) bInd = ancestor.chromosomeList.index(chrB) if len(tempB) > 0: ancestor.chromosomeList[bInd] = tempB else: ancestor.chromosomeList.pop(bInd) def split( ancestor): n = ancestor.getName() chromosome = rn.choice(ancestor.chromosomeList) i = rn.randrange(1,len(chromosome)) a,b = chromosome[:i], chromosome[i:] k = ancestor.chromosomeList.index( chromosome) ancestor.chromosomeList[k] = a ancestor.chromosomeList.append(b) if mod == "REVERSAL": reversal( ancestor ) elif mod == "TRANSLOCATION": if len(ancestor.chromosomeList) > 1 and rn.random > 0.1: translocate( ancestor ) else: split( ancestor ) return ancestor def evolve(self, evolutionRate=0.2): assert self.tree.isBinary() for tip in self.tree.getTips(): if rn.random() < evolutionRate: newGenome = Genome( genome=tip.genome, name=str(rn.randint(0,2**64)) ) self.mutate( newGenome ) if rn.random() < evolutionRate: self.mutate( tip.genome ) tip.genome.getName( name=str(rn.randint(0,2**64))) tip.addConnection( tip.genome) tip.addConnection( newGenome) if self.firstRound and len(self.tree.subs) == 2: self.firstRound = False (a,b) = self.tree.subs a.addConnection(b) a.breakConnection( self.tree ) b.breakConnection( self.tree) self.tree = a assert len( self.tree.getTips() ) == 2 assert self.tree.isBinary() assert self.tree.isBinary()
