def sample_arg_dsmc(k, popsize, rho, recombmap=None,
start=0.0, end=0.0, times=None, times2=None,
init_tree=None, names=None, make_names=True):
"""
Returns an ARG sampled from the Discrete Sequentially Markov Coalescent
k -- chromosomes
popsize -- effective population size
rho -- recombination rate (recombinations / site / generation)
recombmap -- map for variable recombination rate
start -- staring chromosome coordinate
end -- ending chromsome coordinate
names -- names to use for leaves (default: None)
make_names -- make names using strings (default: True)
"""
if times is None:
maxtime = 160000
delta = .01
ntimes = 20
times = argweaver.get_time_points(ntimes, maxtime, delta)
it = sample_dsmc_sprs(
k, popsize, rho, recombmap=recombmap,
start=start, end=end, times=times, times2=times2,
init_tree=init_tree, names=names, make_names=make_names)
tree = it.next()
arg = arglib.make_arg_from_sprs(tree, it)
return arg
def sample_arg_dsmc(k, popsize, rho, recombmap=None,
start=0.0, end=0.0, times=None,
init_tree=None, names=None, make_names=True):
"""
Returns an ARG sampled from the Discrete Sequentially Markov Coalescent
k -- chromosomes
popsize -- effective population size
rho -- recombination rate (recombinations / site / generation)
recombmap -- map for variable recombination rate
start -- staring chromosome coordinate
end -- ending chromsome coordinate
names -- names to use for leaves (default: None)
make_names -- make names using strings (default: True)
"""
if times is None:
maxtime = 160000
delta = .01
ntimes = 20
times = argweaver.get_time_points(ntimes, maxtime, delta)
it = sample_dsmc_sprs(
k, popsize, rho, recombmap=recombmap,
start=start, end=end, times=times,
init_tree=init_tree, names=names, make_names=make_names)
tree = it.next()
arg = arglib.make_arg_from_sprs(tree, it)
return arg
def smc2arg(smc):
"""
Convert SMC to ARG.
NOTE: SMC is 1-index and ARG is 0-index
"""
it = smc2sprs(smc)
tree = it.next()
arg = arglib.make_arg_from_sprs(tree, it)
return arg
def smc2arg(smc):
"""
Convert SMC to ARG.
NOTE: SMC is 1-index and ARG is 0-index
"""
it = smc2sprs(smc)
tree = it.next()
arg = arglib.make_arg_from_sprs(tree, it)
return arg
def treeset2arg(ptrees, ages, sprs, blocks, names, times):
"""
Converts a ptree representation into an ARG.
"""
seqlen = blocks[-1][1]
arg = arglib.ARG(0, seqlen)
# build first tree
lookup = {}
for i, p in enumerate(ptrees[0]):
if i < len(names):
# make leaf
lookup[i] = arg.new_node(names[i], age=times[ages[0][i]],
event="gene")
else:
lookup[i] = arg.new_node(age=times[ages[0][i]], event="coal")
# set parents of new tree
for i, p in enumerate(ptrees[0]):
node = lookup[i]
if p != -1:
node.parents.append(lookup[p])
node.parents[0].children.append(node)
else:
arg.root = node
# convert sprs
sprs2 = []
for i, (rinode, ritime, cinode, citime) in enumerate(sprs):
pos = blocks[i][0] # - 1
# check for null spr
if rinode == -1:
continue
# make local tree
ptree = ptrees[i-1]
tree = treelib.Tree()
lookup = []
for j in range(len(ptree)):
if j < len(names):
lookup.append(tree.new_node(names[j]))
else:
lookup.append(tree.new_node())
for j in range(len(ptree)):
if ptree[j] != -1:
parent = lookup[ptree[j]]
tree.add_child(parent, lookup[j])
else:
tree.root = lookup[j]
# get leaf sets
rleaves = lookup[rinode].leaf_names()
cleaves = lookup[cinode].leaf_names()
assert ritime >= ages[i-1][rinode], (pos, ritime, ages[i-1][rinode])
assert citime >= ages[i-1][cinode], (pos, citime, ages[i-1][cinode])
sprs2.append((pos, (rleaves, times[ritime]), (cleaves, times[citime])))
arglib.make_arg_from_sprs(arg, sprs2)
return arg
