#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()