"right_value < ? AND name_class == 'scientific name' AND node_rank LIKE ?", (left_value, right_value, rank.strip()))
return [row[0] for row in db_cursor.fetchall()]
# for row in db_cursor.fetchall():
# print row
# return []
if len(sys.argv) < 4:
print("usage: fill_tips_from_taxonomy.py <treefile> <taxonomydb> <outfile>")
sys.exit(0)
tree = None
with open(sys.argv[1],"r") as intree_file:
tree = newick3.parse(intree_file.readline())
conn = sqlite3.connect(sys.argv[2])
c = conn.cursor()
for tip in tree.leaves():
for child_name in get_child_taxa(tip.label, "genus", c):
child = phylo3.Node()
child.label = child_name
child.istip = True
# print child.label
tip.add_child(child)
# print([t.label for t in tip.children])
with open(sys.argv[3],"w") as outfile:
# print(newick3.to_string(tree)+";")
outfile.write(newick3.to_string(tree)+";")
all_found_l = False
else:
any_found_l = True
# not sure if having two options here should have any effect... i think they are the same for practical purposes
if (all_found_r and not any_found_l):
# result["identical_side"] = "R"
r_tree_string = "((" + ",".join(result["seq_labels"]["R"]) + "),(" + ",".join(result["seq_labels"]["L"]) + "));"
elif (all_found_l and not any_found_r):
# result["identical_side"] = "L"
r_tree_string = "((" + ",".join(result["seq_labels"]["L"]) + "),(" + ",".join(result["seq_labels"]["R"]) + "));"
result_tree = newick3.parse(r_tree_string)
# write the result topology to the set of observed topologies for this node
topo_file.write(newick3.to_string(result_tree)+";\n")
# get the ICA score from phyx
pxbp_outfile = "temp_pxbp_out." + node.label
pxbp_args = ["pxbp", "-t", topo_file_name, ">", pxbp_outfile]
subprocess.call(" ".join(pxbp_args),shell=True)
# set default values: if we don't find a score in the pxbp output then this bipart is never observed
ica = "-1"
freq = "0"
with open(pxbp_outfile,"r") as pxbp_result:
for line in pxbp_result:
parts = line.split("\t")
if len(parts) > 1:
while len(tree.children) < 2:
# prune knuckles at the root of the tree if necessary
only_child = tree.children[0]
only_child.parent = None
only_child.isroot = True
tree = only_child
# cannot edit tree while traversing, so just record knuckles as we go
knuckles = []
# first find the knuckles
for parent in tree.iternodes(phylo3.PREORDER):
if parent.istip:
continue
logfile.write("node '" + (
str(parent.label) if parent.label != None else str(parent)) +
"' has " + str(len(parent.children)) + " children\n")
if len(parent.children) == 1:
logfile.write("\tthis node will be pruned\n")
knuckles.append(parent)
# now graft them out
for k in knuckles:
k.parent.add_child(k.children[0])
k.parent.remove_child(k)
print newick3.to_string(tree) + ";"
"error: mrca in master tree must define a biparition, not a multifurcation!"
)
# get the bipart *below* the master mrca, since all target taxa are contained by it
master_bipart = get_bipart(master_mrca.children[0])
# print("master bipart: " + get_string(master_bipart))
# first check if the current root is already compatible, if so just reiterate original topology
# THIS FAILS when there is a polytomy at the root of the input tree
# if is_compatible(get_bipart(target), master_bipart):
# print(newick3.to_string(target)+";\n")
# sys.exit(0)
for test_root in target.descendants():
test_bipart = get_bipart(test_root)
if is_compatible(test_bipart, master_bipart):
# just for debugging. otherwise result with not be valid newick
# print("found node in input tree compatible with root node in master: " + get_string(test_bipart))
# print("old topology is: " + newick3.to_string(test_root))
rooted_tree = phylo3.get_tree_rooted_on(test_root)
print(newick3.to_string(rooted_tree) + ";\n")
sys.exit(0)
# if we got here, then there was no bipartition in the input tree compatible with the root bipart in the master
# ...assuming there are not bugs in script that might otherwise get here...
sys.exit(
"error: could not root tree. there may not be a bipartition in the target that is compatible with the root bipart in master!"
)
#!/usr/bin/env python
if __name__ == '__main__':
import newick3, phylo3, sys
if len(sys.argv) < 2:
print "usage: print_tip_names <treefile>"
sys.exit()
treefname = sys.argv[1]
treefile = open(treefname, "r")
for line in treefile:
tree = newick3.parse(line)
print(newick3.to_string(tree, use_node_labels=False))
new_node.add_child(nodes.pop())
if make_brlens:
new_node.length = random.random() * max_brlen
nodes.append(new_node)
return nodes[0]
if __name__ == "__main__":
description = "make a random tree with X tips"
parser = argparse.ArgumentParser(description=description)
parser.add_argument("-x", "--number-of-tips", type=int, nargs=1, required=False, help="The number of tips. If this is specified, tip labels will be numbers. Either this or a set of input tip labels must be specified.")
parser.add_argument("-l", "--tip-labels", nargs='*', required=False, help="A set of tip labels for the random tree. If this is not set, then the number of tips must be specified, and tip labels will be numbers.")
parser.add_argument("-m", "--max-branch-length", type=float, nargs=1, required=False, help="The upper bound for creating randomized branch lengths. If not set, branch lengths will be zero. This argument cannot be used in conjuction with the TREE_AGE argument.")
args = parser.parse_args()
if (args.number_of_tips != None and args.tip_labels != None) or (args.number_of_tips == None and args.tip_labels == None):
sys.exit("You must specify either the number of tips or the tip labels, but not both")
tip_labels = args.tip_labels if args.tip_labels != None else [str(i) for i in range(1, args.number_of_tips[0]+1)]
max_brlen = args.max_branch_length[0] if args.max_branch_length != None else 0
make_brlens = True if max_brlen > 0 else False
print(newick3.to_string(nodes[0], use_branch_lengths=make_brlens) + ";")
tree = newick3.parse(line)
while len(tree.children) < 2:
# prune knuckles at the root of the tree if necessary
only_child = tree.children[0]
only_child.parent = None
only_child.isroot = True
tree = only_child
# cannot edit tree while traversing, so just record knuckles as we go
knuckles = []
# first find the knuckles
for parent in tree.iternodes(phylo3.PREORDER):
if parent.istip:
continue
logfile.write("node '" + (str(parent.label) if parent.label != None else str(parent)) + "' has " + str(len(parent.children)) + " children\n")
if len(parent.children) == 1:
logfile.write("\tthis node will be pruned\n")
knuckles.append(parent)
# now graft them out
for k in knuckles:
k.parent.add_child(k.children[0])
k.parent.remove_child(k)
print newick3.to_string(tree) + ";"
)
parser.add_argument(
"-m",
"--max-branch-length",
type=float,
nargs=1,
required=False,
help=
"The upper bound for creating randomized branch lengths. If not set, branch lengths will be zero. This argument cannot be used in conjuction with the TREE_AGE argument."
)
args = parser.parse_args()
if (args.number_of_tips != None
and args.tip_labels != None) or (args.number_of_tips == None
and args.tip_labels == None):
sys.exit(
"You must specify either the number of tips or the tip labels, but not both"
)
tip_labels = args.tip_labels if args.tip_labels != None else [
str(i) for i in range(1, args.number_of_tips[0] + 1)
]
max_brlen = args.max_branch_length[
0] if args.max_branch_length != None else 0
make_brlens = True if max_brlen > 0 else False
print(newick3.to_string(nodes[0], use_branch_lengths=make_brlens) + ";")
# get one node at random from the tree
n = random.sample(list(get_nodes(tree)), 1)[0]
# create a new internal node to be the parent of the tip we're about to add
new_parent = phylo3.Node()
if n.parent == None: # root case: new parent becomes the new root of the tree
tree = new_parent
else: # non-root case: randomly place new parent on the branch leading to n
p = n.parent
p.remove_child(n)
p.add_child(new_parent)
# reattach n to the new parent
new_parent.add_child(n)
# update branch lengths
new_parent.length = random.uniform(min_branch_length, n.length - min_branch_length)
n.length = n.length - new_parent.length
# add the new tip as a child of the new parent
new_tip = phylo3.Node()
new_tip.label = name
new_tip.istip = True
new_tip.length = new_parent.depth - new_parent.length
new_parent.add_child(new_tip)
print(newick3.to_string(tree))
#!/usr/bin/env python
import sys, newick3, phylo3
if len(sys.argv) < 3:
sys.exit("usage: extract_subtree.py <treefile> <mrca1> <mrca2>")
tree_file_name = sys.argv[1]
mrca1 = sys.argv[2].strip()
mrca2 = sys.argv[3].strip()
with open(tree_file_name) as treefile:
tree = newick3.parse(treefile.readline())
print newick3.to_string(phylo3.get_mrca(tree, [mrca1, mrca2]))
def validate_tree_type(t):
if t == 'pectinate':
return get_pectinate_tree
elif t == 'balanced':
return get_balanced_tree
else:
sys.exit('invalid tree type: ' + t)
if __name__ == '__main__':
parser = argparse.ArgumentParser('')
parser.add_argument('-n', '--number-of-tips', type=int, required=True, \
help='The number of tips to be in the final tree')
parser.add_argument('-b', '--mean-branch-length', type=float, required=True, \
help='The length to be used for internal branches')
parser.add_argument('-t', '--tree-generator-method', type=validate_tree_type, required=True, \
help='The type of tree to generate. Must be either "pectinate" or "balanced".')
args = parser.parse_args()
sys.setrecursionlimit(args.number_of_tips+100)
# currently just supports constant rate
t = args.tree_generator_method(args.number_of_tips, lambda x: x, args.mean_branch_length)
print(newick3.to_string(t) + ';')
# not sure if having two options here should have any effect... i think they are the same for practical purposes
if (all_found_r and not any_found_l):
# result["identical_side"] = "R"
r_tree_string = "((" + ",".join(
result["seq_labels"]["R"]) + "),(" + ",".join(
result["seq_labels"]["L"]) + "));"
elif (all_found_l and not any_found_r):
# result["identical_side"] = "L"
r_tree_string = "((" + ",".join(
result["seq_labels"]["L"]) + "),(" + ",".join(
result["seq_labels"]["R"]) + "));"
result_tree = newick3.parse(r_tree_string)
# write the result topology to the set of observed topologies for this node
topo_file.write(newick3.to_string(result_tree) + ";\n")
# get the ICA score from phyx
pxbp_outfile = "temp_pxbp_out." + node.label
pxbp_args = ["pxbp", "-t", topo_file_name, ">", pxbp_outfile]
subprocess.call(" ".join(pxbp_args), shell=True)
# set default values: if we don't find a score in the pxbp output then this bipart is never observed
ica = "-1"
freq = "0"
with open(pxbp_outfile, "r") as pxbp_result:
for line in pxbp_result:
parts = line.split("\t")
if len(parts) > 1:
# get one node at random from the tree
n = random.sample(list(get_nodes(tree)), 1)[0]
# create a new internal node to be the parent of the tip we're about to add
new_parent = phylo3.Node()
if n.parent == None: # root case: new parent becomes the new root of the tree
tree = new_parent
else: # non-root case: randomly place new parent on the branch leading to n
p = n.parent
p.remove_child(n)
p.add_child(new_parent)
# reattach n to the new parent
new_parent.add_child(n)
# update branch lengths
new_parent.length = random.uniform(min_branch_length,
n.length - min_branch_length)
n.length = n.length - new_parent.length
# add the new tip as a child of the new parent
new_tip = phylo3.Node()
new_tip.label = name
new_tip.istip = True
new_tip.length = new_parent.depth - new_parent.length
new_parent.add_child(new_tip)
print(newick3.to_string(tree))