def test_est_popsize(self):
"""
Fully sample an ARG from stratch using API
"""
k = 50
rho = 1.5e-8
mu = 2.5e-8
length = int(1e6)
times = arghmm.get_time_points(ntimes=30, maxtime=200000)
popsize = 1e4
refine = 0
util.tic("sim ARG")
arg = arghmm.sample_arg_dsmc(k, 2 * popsize,
rho, start=0, end=length, times=times)
#arg = arglib.sample_arg_smc(k, 2 * popsize,
# rho, start=0, end=length)
#arg = arglib.sample_arg(k, 2 * popsize, rho, start=0, end=length)
util.toc()
x = []
for tree in arglib.iter_marginal_trees(arg):
arglib.remove_single_lineages(tree)
x.append(mle_popsize_tree(tree, mintime=0))
p = plot(x, ymin=0)
p.plot([0, len(x)], [popsize, popsize], style='lines')
pause()
def test_est_popsize(self):
"""
Fully sample an ARG from stratch using API
"""
k = 50
rho = 1.5e-8
mu = 2.5e-8
length = int(1e6)
times = arghmm.get_time_points(ntimes=30, maxtime=200000)
popsize = 1e4
refine = 0
util.tic("sim ARG")
arg = arghmm.sample_arg_dsmc(k, 2 * popsize,
rho, start=0, end=length, times=times)
#arg = arglib.sample_arg_smc(k, 2 * popsize,
# rho, start=0, end=length)
#arg = arglib.sample_arg(k, 2 * popsize, rho, start=0, end=length)
util.toc()
x = []
for tree in arglib.iter_marginal_trees(arg):
arglib.remove_single_lineages(tree)
x.append(mle_popsize_tree(tree, mintime=0))
p = plot(x, ymin=0)
p.plot([0, len(x)], [popsize, popsize], style='lines')
pause()
def show_marginal_trees(arg, mut=None):
win = summon.Window()
x = 0
step = 2
treewidth = len(list(arg.leaves())) + step
def trans_camera(win, x, y):
v = win.get_visible()
win.set_visible(v[0]+x, v[1]+y, v[2]+x, v[3]+y, "exact")
win.set_binding(input_key("]"), lambda : trans_camera(win, treewidth, 0))
win.set_binding(input_key("["), lambda : trans_camera(win, -treewidth, 0))
blocks = arglib.iter_recomb_blocks(arg)
for tree, block in izip(arglib.iter_marginal_trees(arg), blocks):
pos = block[0]
print pos
leaves = sorted((x for x in tree.leaves()), key=lambda x: x.name)
layout = layout_arg(tree, leaves)
win.add_group(
translate(x, 0, color(1,1,1),
draw_tree(tree, layout),
text_clip(
"%d-%d" % (block[0], block[1]),
treewidth*.05, 0,
treewidth*.95, -max(l[1] for l in layout.values()),
4, 20,
"center", "top")))
# mark responsible recomb node
for node in tree:
if pos != 0.0 and node.pos == pos:
nx, ny = layout[node]
win.add_group(draw_mark(x + nx, ny))
# draw mut
if mut:
for node, parent, mpos, t in mut:
if (node.name in tree and node.name != tree.root.name and
block[0] < mpos < block[1]):
nx, ny = layout[tree[node.name]]
win.add_group(draw_mark(x + nx, t, col=(0,0,1)))
if node.name in tree and tree[node.name].parents:
nx, ny = layout[tree[node.name]]
py = layout[tree[node.name].parents[0]][1]
start = arg[node.name].data["ancestral"][0][0]
win.add_group(lines(color(0,1,0),
x+nx, ny, x+nx, py,
color(1,1,1)))
x += treewidth
win.set_visible(* win.get_root().get_bounding() + ("exact",))
return win
def show_marginal_trees(arg, mut=None):
win = summon.Window()
x = 0
step = 2
treewidth = len(list(arg.leaves())) + step
def trans_camera(win, x, y):
v = win.get_visible()
win.set_visible(v[0]+x, v[1]+y, v[2]+x, v[3]+y, "exact")
win.set_binding(input_key("]"), lambda : trans_camera(win, treewidth, 0))
win.set_binding(input_key("["), lambda : trans_camera(win, -treewidth, 0))
blocks = arglib.iter_recomb_blocks(arg)
for tree, block in zip(arglib.iter_marginal_trees(arg), blocks):
pos = block[0]
print(pos)
leaves = sorted((x for x in tree.leaves()), key=lambda x: x.name)
layout = layout_arg(tree, leaves)
win.add_group(
translate(x, 0, color(1,1,1),
draw_tree(tree, layout),
text_clip(
"%d-%d" % (block[0], block[1]),
treewidth*.05, 0,
treewidth*.95, -max(l[1] for l in list(layout.values())),
4, 20,
"center", "top")))
# mark responsible recomb node
for node in tree:
if pos != 0.0 and node.pos == pos:
nx, ny = layout[node]
win.add_group(draw_mark(x + nx, ny))
# draw mut
if mut:
for node, parent, mpos, t in mut:
if (node.name in tree and node.name != tree.root.name and
block[0] < mpos < block[1]):
nx, ny = layout[tree[node.name]]
win.add_group(draw_mark(x + nx, t, col=(0,0,1)))
if node.name in tree and tree[node.name].parents:
nx, ny = layout[tree[node.name]]
py = layout[tree[node.name].parents[0]][1]
start = arg[node.name].data["ancestral"][0][0]
win.add_group(lines(color(0,1,0),
x+nx, ny, x+nx, py,
color(1,1,1)))
x += treewidth
win.set_visible(* win.get_root().get_bounding() + ("exact",))
return win
def get_mutation_split_tracks(arg, mut_splits, mut_pos):
mut_splits_set = set(mut_splits)
mut_split_tracks = defaultdict(lambda: [])
# find regions for splits
i = 0
for block, tree in zip(arglib.iter_recomb_blocks(arg),
arglib.iter_marginal_trees(arg)):
for node in tree:
if len(node.children) != 2 or node.children[0] == node.children[1]:
continue
split = tuple(sorted(tree.leaf_names(node)))
if split in mut_splits_set:
regions = mut_split_tracks[split]
if len(regions) > 0 and regions[-1][1] == block[0]:
# extend region
regions[-1] = (regions[-1][0], block[1])
else:
# add new region
regions.append(block)
# keep only tracks who have a mutation in their interval
mut_tracks = []
for i in range(len(mut_pos)):
for region in mut_split_tracks[mut_splits[i]]:
if region[0] < mut_pos[i] < region[1]:
a = util.binsearch(mut_pos, region[0])[0]
a = a if a is not None else -.5
b = util.binsearch(mut_pos, region[1])[1]
b = b if b is not None else len(mut_pos)-.5
mut_tracks.append((a, b))
break
else:
assert False, i
return mut_tracks
def get_mutation_split_tracks(arg, mut_splits, mut_pos):
mut_splits_set = set(mut_splits)
mut_split_tracks = defaultdict(lambda: [])
# find regions for splits
i = 0
for block, tree in izip(arglib.iter_recomb_blocks(arg), arglib.iter_marginal_trees(arg)):
for node in tree:
if len(node.children) != 2 or node.children[0] == node.children[1]:
continue
split = tuple(sorted(tree.leaf_names(node)))
if split in mut_splits_set:
regions = mut_split_tracks[split]
if len(regions) > 0 and regions[-1][1] == block[0]:
# extend region
regions[-1] = (regions[-1][0], block[1])
else:
# add new region
regions.append(block)
# keep only tracks who have a mutation in their interval
mut_tracks = []
for i in xrange(len(mut_pos)):
for region in mut_split_tracks[mut_splits[i]]:
if region[0] < mut_pos[i] < region[1]:
a = util.binsearch(mut_pos, region[0])[0]
a = a if a is not None else -0.5
b = util.binsearch(mut_pos, region[1])[1]
b = b if b is not None else len(mut_pos) - 0.5
mut_tracks.append((a, b))
break
else:
assert False, i
return mut_tracks