def _treeFromTimes(times, order = None) :
""" Build a biopython tree from intra-coalescent intervals in times.
Without an order, the joining is random. With order, use the given ordering
supplied as a sequence of pairs, each pair is two indices picked to join.
"""
if order is not None :
order = list(order)
assert len(times) == len(order)
n = len(times) + 1
tb = TreeBuilder()
taxa = [[tb.createLeaf("ID%d" % k), 0.0] for k in range(n)]
height = 0.0
for t in reversed(times) :
i,j = order.pop(0) if order else \
random.sample(range(len(taxa)), 2)
l1,l2 = taxa[i],taxa[j]
height += t
nd = tb.mergeNodes([[x[0], height - x[1]] for x in (l1,l2)])
taxa.pop(max(i,j))
taxa[min(i,j)] = [nd, height]
return tb.finalize(taxa[0][0])
def mau2Tree(mauTree) : """ Convert a tree in Mau representation to a BioPython Nexus Tree object.""" t = TreeBuilder() rep, h, nid = _mau2treeInternal(mauTree[0], array(mauTree[1]), mauTree[2]) r = _mau2NexusInternal((rep, 0), t) return t.finalize(r[0])
def simulateGeneTree(sTree) :
""" Simulate one gene tree under species (spp) tree C{sTree}.
Return a pair of tree and root height.
"""
nh = nodeHeights(sTree)
simTree = TreeBuilder()
t,rootHeight = _simulateGeneTreeForNode(sTree, sTree.root, simTree, nh)[0]
t = simTree.finalize(t)
return (t,rootHeight)
def _build(nodes, weight=1.0, rooted=True, name='') :
# name/support ignored
tb = TreeBuilder(weight=weight, rooted = rooted, name=name)
t = [None]*len(nodes)
for k, x in enumerate(nodes):
if x[2] is None or len(x[2]) == 0:
t[k] = tb.createLeaf(x[0])
else :
t[k] = tb.mergeNodes([ [t[l], nodes[l][1]] for l in x[2]])
if x[3] is not None:
t[k].data.attributes = dict(x[3])
return tb.finalize(t[-1])
def sampleCoalescentTree(demog, labels) :
""" Build a tree under the coalescent model using given demographic."""
if isinstance(labels, int) :
labels = ["tip%03d" % k for k in range(int(labels))]
else :
assert all([isinstance(s, str) for s in labels])
n = len(labels)
times= [0,]*n
lineageInfo = len(labels)
# times = reduce(operator.add, [[t,]*n for n,t in lineageInfo])
#assert len(labels) == len(times)
at = getArrivalTimes(demog, lineageInfo)
tb = TreeBuilder()
nodes = [tb.createLeaf(l) for l in labels]
strees = zip(nodes, times)
for t in at :
# find 2 labels with times < t and coalesce
available = [k for k in range(len(strees)) if strees[k][1] < t]
assert len(available) > 1,(available,t,at,strees)
i,j = random.sample(available, 2)
l1,l2 = strees[i],strees[j]
n = tb.mergeNodes([[x[0], t - x[1]] for x in (l1,l2)])
strees.pop(max(i,j))
strees.pop(min(i,j))
strees.insert(0, (n, t))
assert len(strees) == 1
return tb.finalize(strees[0][0])
