def _reroot_helper(self, gtree, newCopy=True, returnEdge=False):
"""
Yields rerooted trees.
Adapted from phylo.recon_root.
"""
# make a consistent unrooted copy of gene tree
if newCopy:
gtree = gtree.copy()
if len(gtree.leaves()) == 2:
raise StopIteration
oldroot = gtree.root.name
treelib.unroot(gtree, newCopy=False)
treelib.reroot(gtree,
gtree.nodes[sorted(gtree.leaf_names())[0]].parent.name,
onBranch=False, newCopy=False)
# make rerooting order consistent using hash ordering
phylo.hash_order_tree(gtree, self.gene2species)
# get list of edges to root on
edges = []
def walk(node):
edges.append((node, node.parent))
if not node.is_leaf():
node.recurse(walk)
edges.append((node, node.parent))
for child in gtree.root.children:
walk(child)
# try initial root
treelib.reroot(gtree, edges[0][0].name, newCopy=False)
gtree.rename(gtree.root.name, oldroot)
if returnEdge:
yield gtree, edges[0]
else:
yield gtree
rootedge = sorted(edges[0])
# try rerooting on everything
for edge in edges[1:]:
if sorted(edge) == rootedge:
continue
rootedge = sorted(edge)
node1, node2 = edge
if node1.parent != node2:
node1, node2 = node2, node1
assert node1.parent == node2, "%s %s" % (node1.name, node2.name)
# new root and cost
treelib.reroot(gtree, node1.name, newCopy=False, keepName=True)
if returnEdge:
yield gtree, edge
else:
yield gtree
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 _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)
