def prob_locus_coal_recon_topology_samples(
coal_tree, coal_recon,
locus_tree, locus_recon, locus_events, locus_popsizes,
stree, stimes,
daughters,
birth, death, nsamples, pretime=None, premean=100.0):
if pretime is None:
pretime = -1
ptree, nodes, nodelookup = dlcoal.make_ptree(coal_tree)
pltree, lnodes, lnodelookup = dlcoal.make_ptree(locus_tree)
pstree, snodes, snodelookup = dlcoal.make_ptree(stree)
crecon2 = dlcoal.make_recon_array(
coal_tree, coal_recon, nodes, lnodelookup)
lrecon2 = dlcoal.make_recon_array(
locus_tree, locus_recon, lnodes, snodelookup)
levents2 = dlcoal.make_events_array(lnodes, locus_events)
locus_popsizes = compbio.coal.init_popsizes(locus_tree, locus_popsizes)
popsizes2 = [locus_popsizes[lnode.name] for lnode in lnodes]
stimes2 = [stimes[snode] for snode in snodes]
daughters2 = [lnodelookup[lnode] for lnode in daughters]
p = dlcoal.dlcoalc.prob_locus_coal_recon_topology_samples(
c_list(c_int, ptree), len(nodes), c_list(c_int, crecon2),
c_list(c_int, pltree), len(lnodes),
c_list(c_int, lrecon2), c_list(c_int, levents2),
c_list(c_double, popsizes2),
c_list(c_int, pstree), len(snodes), c_list(c_double, stimes2),
c_list(c_int, daughters2), len(daughters),
birth, death, nsamples, pretime, premean)
return p
def prob_multicoal_recon_topology(tree, recon, stree, n,
lineages=None, top_stats=None):
ptree, nodes, nodelookup = dlcoal.make_ptree(tree)
pstree, snodes, snodelookup = dlcoal.make_ptree(stree)
recon2 = dlcoal.make_recon_array(tree, recon, nodes, snodelookup)
popsizes = compbio.coal.init_popsizes(stree, n)
popsizes2 = [popsizes[snode.name] for snode in snodes]
sdists = [snode.dist for snode in snodes]
p = dlcoal.dlcoalc.prob_multicoal_recon_topology(
c_list(c_int, ptree), len(nodes), c_list(c_int, recon2),
c_list(c_int, pstree), len(snodes), c_list(c_double, sdists),
c_list(c_double, popsizes2))
return p
def prob_locus_coal_recon_topology(tree, recon, locus_tree, n, daughters):
ptree, nodes, nodelookup = dlcoal.make_ptree(tree)
pltree, lnodes, lnodelookup = dlcoal.make_ptree(locus_tree)
recon2 = dlcoal.make_recon_array(tree, recon, nodes, lnodelookup)
popsizes = compbio.coal.init_popsizes(locus_tree, n)
popsizes2 = [popsizes[lnode.name] for lnode in lnodes]
ltimes = treelib.get_tree_timestamps(locus_tree)
ltimes2 = [ltimes[lnode] for lnode in lnodes]
daughters2 = [lnodelookup[lnode] for lnode in daughters]
p = dlcoal.dlcoalc.prob_locus_coal_recon_topology(
c_list(c_int, ptree), len(nodes), c_list(c_int, recon2),
c_list(c_int, pltree), 0, len(lnodes),
c_list(c_double, popsizes2), c_list(c_double, ltimes2),
c_list(c_int, daughters2), len(daughters))
return p
def prob_dup_loss(tree, stree, recon, events, duprate, lossrate):
"""Returns the topology prior of a gene tree"""
if dlcoal.dlcoalc:
if events is None:
events = phylo.label_events(tree, recon)
ptree, nodes, nodelookup = dlcoal.make_ptree(tree)
pstree, snodes, snodelookup = dlcoal.make_ptree(stree)
ctree = dlcoal.tree2ctree(tree)
cstree = dlcoal.tree2ctree(stree)
recon2 = dlcoal.make_recon_array(tree, recon, nodes, snodelookup)
events2 = dlcoal.make_events_array(nodes, events)
doomtable = c_list(c_double, [0] * len(stree.nodes))
dlcoal.dlcoalc.calcDoomTable(cstree, duprate, lossrate, doomtable)
p = dlcoal.dlcoalc.birthDeathTreePriorFull(ctree, cstree,
c_list(c_int, recon2),
c_list(c_int, events2),
duprate, lossrate, doomtable)
dlcoal.dlcoalc.deleteTree(ctree)
dlcoal.dlcoalc.deleteTree(cstree)
return p
else:
if "dlcoal_python_fallback" not in globals():
print >>sys.stderr, "warning: using python code instead of native"
globals()["dlcoal_python_fallback"] = 1
# spidir libs
import spidir
from spidir import topology_prior
return topology_prior.dup_loss_topology_prior(
tree, stree, recon, duprate, lossrate,
events=events)