#simulating brownian motion along entire tree
t = treegenerator.simulate_brownian(t, sigma, dimension)
#calculating max coordinate to give the bounds of habitat for phyrex
max_coordinate = 0
for node in t.preorder_node_iter():
max_coordinate = max(max_coordinate, abs(node.X))
if dimension == 2:
max_coordinate = max(max_coordinate, abs(node.Y))
#line of code for writing xml file for full sampling (this is not needed necessary)
beastxmlwriter.write_BEAST_xml(
t,
i,
dimension,
mcmc,
log_every,
beast_input_string="output/beast/no_sampling/beast_input/beast",
beast_output_string="output/beast/no_sampling/beast_output/beast")
if generate_sample_files:
for output_index in range(1, num_sampling + 1):
if output_index == 1:
sampled_t = sampling.sample_unbiased(t,
dimension,
sample_ratio=sample_ratio)
elif output_index == 2:
sampled_t = sampling.sample_biased_most_central(
t, dimension, sample_ratio=sample_ratio)
elif output_index == 3:
if leaf_index < 10:
leaf_label = "s000" + str(leaf_index)
elif leaf_index < 100:
leaf_label = "s00" + str(leaf_index)
elif leaf_index < 1000:
leaf_label = "s0" + str(leaf_index)
node = tree.find_node_with_taxon_label(leaf_label)
node.X = a[leaf_index][0]
node.Y = a[leaf_index][1]
node.annotations.add_bound_attribute("X")
node.annotations.add_bound_attribute("Y")
node.annotations.add_bound_attribute("time")
beastxmlwriter.write_BEAST_xml(
tree,
index,
dimension=2,
mcmc=10000,
log_every=10,
beast_input_string="output/beast/LV/beast_input/beast",
beast_output_string="output/beast/LV/beast_output/beast")
discs_phyrexxmlwriter.write_phyrex_input(
tree,
index,
input_string="output/phyrex/LV/phyrex_input/",
output_string="output/phyrex/LV/phyrex_output/",
bound=L)
os.system(
'ulimit -c unlimited; beast -overwrite -seed 123456795 "output/beast/LV/beast_input/beast'
+ str(index) + '.xml"')
#line to run BEAST
beastxmlwriter.write_BEAST_xml_corrected(
tree,
sampled_t,
d,
i=i,
mcmc=10000000,
log_every=1000,
beast_input_string="output/c_beast/beast_input/beast",
beast_output_string="output/c_beast/beast_output/beast",
other_sample_size=other_sample_size,
seq_len=seq_len)
beastxmlwriter.write_BEAST_xml(
sampled_t,
i=i,
dimension=2,
mcmc=10000,
log_every=10,
beast_input_string="output/c_beast/beast_input/nbeast",
beast_output_string="output/c_beast/beast_output/nbeast")
os.system(
'beast -overwrite -seed 123456795 "output/c_beast/beast_input/beast' +
str(i) + '.xml"')
os.system(
'beast -overwrite -seed 123456795 "output/c_beast/beast_input/nbeast' +
str(i) + '.xml"')
file = open("output/root_data/actual_root" + str(i) + ".txt", "w")
file.write(str(sampled_t.seed_node.X) + '\n')
file.write(str(sampled_t.seed_node.Y) + '\n')
file.close()