def _test_prog_infsites():
make_clean_dir("test/tmp/test_prog_infsites")
run_cmd("""bin/arg-sim \
-k 40 -L 200000 \
-N 1e4 -r 1.5e-8 -m 2.5e-8 --infsites \
--ntimes 20 --maxtime 400e3 \
-o test/tmp/test_prog_infsites/0""")
make_clean_dir("test/tmp/test_prog_infsites/0.sample")
run_cmd("""bin/arg-sample \
-s test/tmp/test_prog_infsites/0.sites \
-N 1e4 -r 1.5e-8 -m 2.5e-8 \
--ntimes 5 --maxtime 100e3 -c 1 \
--climb 0 -n 20 --infsites \
-x 1 \
-o test/tmp/test_prog_infsites/0.sample/out""")
arg = argweaver.read_arg(
"test/tmp/test_prog_infsites/0.sample/out.0.smc.gz")
sites = argweaver.read_sites("test/tmp/test_prog_infsites/0.sites")
print "names", sites.names
print
noncompats = []
for block, tree in arglib.iter_local_trees(arg):
tree = tree.get_tree()
treelib.remove_single_children(tree)
phylo.hash_order_tree(tree)
for pos, col in sites.iter_region(block[0] + 1, block[1] + 1):
assert block[0] + 1 <= pos <= block[1] + 1, (block, pos)
split = sites_split(sites.names, col)
node = arglib.split_to_tree_branch(tree, split)
if node is None:
noncompats.append(pos)
print "noncompat", block, pos, col
print phylo.hash_tree(tree)
print tree.leaf_names()
print "".join(col[sites.names.index(name)]
for name in tree.leaf_names())
print split
print
print "num noncompats", len(noncompats)
def _test_prog_infsites():
make_clean_dir("test/data/test_prog_infsites")
run_cmd("""bin/arg-sim \
-k 40 -L 200000 \
-N 1e4 -r 1.5e-8 -m 2.5e-8 --infsites \
--ntimes 20 --maxtime 400e3 \
-o test/data/test_prog_infsites/0""")
make_clean_dir("test/data/test_prog_infsites/0.sample")
run_cmd("""bin/arg-sample \
-s test/data/test_prog_infsites/0.sites \
-N 1e4 -r 1.5e-8 -m 2.5e-8 \
--ntimes 5 --maxtime 100e3 -c 1 \
--climb 0 -n 20 --infsites \
-x 1 \
-o test/data/test_prog_infsites/0.sample/out""")
arg = argweaver.read_arg(
"test/data/test_prog_infsites/0.sample/out.0.smc.gz")
sites = argweaver.read_sites("test/data/test_prog_infsites/0.sites")
print "names", sites.names
print
noncompats = []
for block, tree in arglib.iter_local_trees(arg):
tree = tree.get_tree()
treelib.remove_single_children(tree)
phylo.hash_order_tree(tree)
for pos, col in sites.iter_region(block[0]+1, block[1]+1):
assert block[0]+1 <= pos <= block[1]+1, (block, pos)
split = sites_split(sites.names, col)
node = arglib.split_to_tree_branch(tree, split)
if node is None:
noncompats.append(pos)
print "noncompat", block, pos, col
print phylo.hash_tree(tree)
print tree.leaf_names()
print "".join(col[sites.names.index(name)]
for name in tree.leaf_names())
print split
print
print "num noncompats", len(noncompats)
def show_tree_track(tree_track, mut=None, show_labels=False,
use_blocks=False, branch_click=None):
"""
tree_track = [((start, end), tree), ...]
"""
def draw_labels(tree, layout):
return group(*
[text_clip(leaf.name, layout[leaf][0], layout[leaf][1],
1, layout[leaf][1] + 1e4, 4, 20, "middle", "left")
for leaf in tree.leaves()])
def branch_hotspot(node, parent, x, y, y2):
def func():
branch_click(node, parent)
return hotspot("click", x-.5, y, x+.5, y2, func)
def print_branch(node, parent):
print "node", node.name
tree_track = iter(tree_track)
if mut:
mut = util.PushIter(mut)
block, tree = tree_track.next()
if branch_click is True:
branch_click = print_branch
win = summon.Window()
treex = 0
step = 2
treewidth = len(list(tree.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))
for block, tree in chain([(block, tree)], tree_track):
pos = block[0]
print pos
layout = treelib.layout_tree(tree, xscale=1, yscale=1)
treelib.layout_tree_vertical(layout, leaves=0)
g = win.add_group(
translate(treex, 0, color(1,1,1),
sumtree.draw_tree(tree, layout,
vertical=True),
(draw_labels(tree, layout) if show_labels else group()),
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")))
clicking = group()
g.append(clicking)
# hotspots
if branch_click:
for node in tree:
if node.parent:
x, y = layout[node]
x2, y2 = layout[node.parent]
clicking.append(branch_hotspot(node, node.parent, x, y, y2))
#win.add_group(clicking)
# draw mut
if mut:
for mpos, age, chroms in mut:
if block[0] < mpos < block[1]:
node = arglib.split_to_tree_branch(tree, chroms)
parent = node.parent
if node and parent:
t = random.uniform(layout[node][1], layout[parent][1])
nx, ny = layout[node]
win.add_group(draw_mark(treex + nx, t, col=(0,0,1)))
elif mpos > block[1]:
mut.push((mpos, age, chroms))
break
treex += treewidth
#win.set_visible(* win.get_root().get_bounding() + ("exact",))
win.home("exact")
return win
def show_tree_track(tree_track,
mut=None,
show_labels=False,
use_blocks=False,
branch_click=None):
"""
tree_track = [((start, end), tree), ...]
"""
def draw_labels(tree, layout):
return group(*[
text_clip(leaf.name, layout[leaf][0], layout[leaf][1], 1,
layout[leaf][1] + 1e4, 4, 20, "middle", "left")
for leaf in tree.leaves()
])
def branch_hotspot(node, parent, x, y, y2):
def func():
branch_click(node, parent)
return hotspot("click", x - .5, y, x + .5, y2, func)
def print_branch(node, parent):
print "node", node.name
tree_track = iter(tree_track)
if mut:
mut = util.PushIter(mut)
block, tree = tree_track.next()
if branch_click is True:
branch_click = print_branch
win = summon.Window()
treex = 0
step = 2
treewidth = len(list(tree.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))
for block, tree in chain([(block, tree)], tree_track):
pos = block[0]
print pos
layout = treelib.layout_tree(tree, xscale=1, yscale=1)
treelib.layout_tree_vertical(layout, leaves=0)
g = win.add_group(
translate(
treex, 0, color(1, 1, 1),
sumtree.draw_tree(tree, layout, vertical=True),
(draw_labels(tree, layout) if show_labels else group()),
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")))
clicking = group()
g.append(clicking)
# hotspots
if branch_click:
for node in tree:
if node.parent:
x, y = layout[node]
x2, y2 = layout[node.parent]
clicking.append(branch_hotspot(node, node.parent, x, y,
y2))
#win.add_group(clicking)
# draw mut
if mut:
for mpos, age, chroms in mut:
if block[0] < mpos < block[1]:
node = arglib.split_to_tree_branch(tree, chroms)
parent = node.parent
if node and parent:
t = random.uniform(layout[node][1], layout[parent][1])
nx, ny = layout[node]
win.add_group(draw_mark(treex + nx, t, col=(0, 0, 1)))
elif mpos > block[1]:
mut.push((mpos, age, chroms))
break
treex += treewidth
#win.set_visible(* win.get_root().get_bounding() + ("exact",))
win.home("exact")
return win
