def simulate_pangenome(ngenes, nisolates, effective_pop_size, gain_rate,
loss_rate, mutation_rate, max_core):
# simulate a phylogeny using the coalscent
sim_tree = treesim.pure_kingman_tree(taxon_namespace=TaxonNamespace(
[str(i) for i in range(1, 1 + nisolates)]),
pop_size=effective_pop_size)
basic_tree = copy.deepcopy(sim_tree)
# simulate gene p/a and mutation
sim_tree = simulate_img_with_mutation(sim_tree,
gain_rate=gain_rate,
loss_rate=loss_rate,
mutation_rate=mutation_rate,
ngenes=ngenes,
max_ncore=max_core)
# get genes and mutations for each isolate
gene_mutations = []
for leaf in sim_tree.leaf_node_iter():
gene_mutations.append([[g, leaf.gene_mutations[g]]
for g in leaf.acc_genes])
return (gene_mutations, basic_tree)
def pure_kingman(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesim.pure_kingman()' function has moved to 'dendropy.simulate.treesim.pure_kingman_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.pure_kingman(...)",
new_construct="from dendropy.simulate import treesim\ntree = treesim.pure_kingman_tree(...)",
)
return treesim.pure_kingman_tree(*args, **kwargs)
def unrooted_pure_kingman_tree(num_taxa,
taxon_namespace=None,
pop_size=1,
rng=None):
if taxon_namespace == None:
taxon_namespace = default_namespace(num_taxa)
tree = pure_kingman_tree(taxon_namespace, pop_size=pop_size, rng=rng)
tree.is_rooted = False
return tree
def pure_kingman(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.treesim.pure_kingman()' function has moved to 'dendropy.simulate.treesim.pure_kingman_tree()'.",
old_construct=
"from dendropy import treesim\ntree = treesim.pure_kingman(...)",
new_construct=
"from dendropy.simulate import treesim\ntree = treesim.pure_kingman_tree(...)"
)
return treesim.pure_kingman_tree(*args, **kwargs)
def main():
"""
Main CLI handler.
"""
parser = argparse.ArgumentParser(description=__description__)
parser.add_argument("--version",
action="version",
version="%(prog)s " + __version__)
parser.add_argument("output_prefix")
parser.add_argument("-k",
"--num-tips",
action="store",
type=int,
default=10,
metavar="NUM-TIPS",
help="Number of samples (default=%(default)s)")
parser.add_argument("-N",
"--pop-size",
"--population-size",
action="store",
type=float,
default=1.0,
metavar="POP-SIZE",
help="Population size (default=%(default)s)")
parser.add_argument("--num-reps",
action="store",
type=int,
default=10,
metavar="NUM-REPS",
help="Number of replicates (default=%(default)s)")
parser.add_argument("-z",
"--random-seed",
type=int,
default=None,
help="Random seed.")
args = parser.parse_args()
if args.random_seed is None:
args.random_seed = random.randint(0, sys.maxsize)
rng = random.Random(args.random_seed)
tns = dendropy.TaxonNamespace(
["G{:03d}".format(i + 1) for i in range(args.num_tips)])
trees = dendropy.TreeList(taxon_namespace=tns)
if args.output_prefix == "-":
coal_out = sys.stdout
else:
coal_out = open("{}.coal.trees".format(args.output_prefix), "w")
for rep_id in range(args.num_reps):
tree = treesim.pure_kingman_tree(taxon_namespace=tns,
pop_size=args.pop_size,
rng=rng)
tree.write(file=coal_out, schema="newick")
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import dendropy
from dendropy.simulate import treesim
taxa = dendropy.TaxonNamespace(
["z1", "z2", "z3", "z4", "z5", "z6", "z7", "z8"])
tree = treesim.pure_kingman_tree(taxon_namespace=taxa, pop_size=10000)
print(tree.as_string(schema="newick"))
print(tree.as_ascii_plot())
def pure_kingman_tree(num_leaves, pop_size):
from dendropy.simulate import treesim
from dendropy import TaxonNamespace
import random as rng
return treesim.pure_kingman_tree(TaxonNamespace([str(i) for i in range(num_leaves)]), pop_size=pop_size, rng=rng).as_string(schema='newick')
#! /usr/bin/env python3
import argparse
from dendropy import TaxonNamespace
from dendropy.simulate import treesim
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-p',
'--population',
required=True,
type=int,
help="Population Size")
parser.add_argument('-n',
'--num_leaves',
required=True,
type=int,
help="Number of Leaves")
args = parser.parse_args()
assert args.num_leaves > 1, "Must have at least 2 leaves"
print(
treesim.pure_kingman_tree(
TaxonNamespace([str(i) for i in range(args.num_leaves)]),
pop_size=args.population).as_string(schema='newick'))
#! /usr/bin/env python
import dendropy
from dendropy.simulate import treesim
taxa = dendropy.TaxonNamespace(["z1", "z2", "z3", "z4", "z5", "z6", "z7", "z8"])
tree = treesim.pure_kingman_tree(
taxon_namespace=taxa,
pop_size=10000)
print(tree.as_string(schema="newick"))
print(tree.as_ascii_plot())
from dendropy import TreeList, TaxonNamespace
from dendropy.simulate import treesim
import os
parser = ArgumentParser('Generate trees of a given size with different algos')
parser.add_argument('-n', type=int, help='Tree size', default=100)
parser.add_argument('-d', type=str, help='Output directory')
args = parser.parse_args()
if not os.path.isdir(args.d):
os.mkdir(args.d)
os.chdir(args.d)
bd2 = TreeList([
treesim.birth_death_tree(birth_rate=1.0,
death_rate=0.5,
num_extant_tips=args.n,
repeat_until_success=True) for _ in range(100)
])
bd2.write_to_path('birth_death2.nwk', schema='newick')
bd5 = TreeList([
treesim.birth_death_tree(birth_rate=1.0,
death_rate=0.2,
num_extant_tips=args.n,
repeat_until_success=True) for _ in range(100)
])
bd5.write_to_path('birth_death5.nwk', schema='newick')
taxa = TaxonNamespace(['T{}'.format(x) for x in range(1, args.n + 1)])
king = TreeList(
[treesim.pure_kingman_tree(taxon_namespace=taxa) for _ in range(100)])
king.write_to_path('kingman.nwk', schema='newick')
def kingman(taxon_count, pop_size):
return treesim.pure_kingman_tree(
taxon_namespace=taxon_namespace_of_count(taxon_count),
pop_size=pop_size)
