def random_yule(self, nspecies=None, names=None):
if names and nspecies:
if not nspecies == len(names):
nspecies = len(names)
elif names and not nspecies:
nspecies = len(names)
elif not names:
if not nspecies:
nspecies = 16
names = taxonnames.names[:nspecies]
if nspecies > len(taxonnames.names):
names.extend(['Sp{0}'.format(i) for i in
range(len(taxonnames.names) + 1, nspecies
+ 1)])
taxon_set = dpy.TaxonSet(names)
tree = treesim.uniform_pure_birth(taxon_set)
newick = '[&R] ' + tree.as_newick_string()
if not newick.endswith(';'):
newick += ';'
return Tree(newick)
parser.add_option(
"-s",
"--seed",
action="store",
dest="seed",
type=long,
default=0,
help="The seed of the random number generator",
)
(opts, args) = parser.parse_args()
num_leaves = opts.num_leaves
if num_leaves < 3:
sys.exit("The number of leaves must be greater than 2")
seed = opts.seed
if seed < 0:
sys.exit("Seed must be positive")
if seed < 1:
seed = time.time()
rng = random.Random()
sys.stderr.write("seed = %ld\n" % seed)
rng.seed(seed)
outstr = sys.stdout
taxa = TaxonSet(["t%d" % i for i in xrange(1, 1 + num_leaves)])
tree = uniform_pure_birth(taxa, rng=rng)
for e in tree.preorder_edge_iter():
e.length = rng.random()
outstr.write("%s;\n" % tree.as_newick_string(preserve_spaces=True))
default=4,
help='The number of leaves to generate.')
parser.add_option('-s',
'--seed',
action='store',
dest='seed',
type=long,
default=0,
help='The seed of the random number generator')
(opts, args) = parser.parse_args()
num_leaves = opts.num_leaves
if num_leaves < 3:
sys.exit("The number of leaves must be greater than 2")
seed = opts.seed
if seed < 0:
sys.exit("Seed must be positive")
if seed < 1:
seed = time.time()
rng = random.Random()
sys.stderr.write("seed = %ld\n" % seed)
rng.seed(seed)
outstr = sys.stdout
taxa = TaxonSet(["t%d" % i for i in xrange(1, 1 + num_leaves)])
tree = uniform_pure_birth(taxa, rng=rng)
for e in tree.preorder_edge_iter():
e.length = rng.random()
outstr.write("%s;\n" % tree.as_newick_string(preserve_spaces=True))
