def calc_histogram(tree_data,
d,
t,
l,
time_it,
normalize=False,
zero_loss=False):
"""
Compute the PDV from a .newick file
:param tree_data <ReconInput> - Output of newickFormatReader.getInput()
:param d <float> - the cost of a duplication
:param t <float> - ^^ transfer
:param l <float> - ^^ loss
:param time_it <bool> - collect timing info
:param normalize <bool> - normalize the histogram by the size of the gene tree
:param zero_loss <bool> - ignore loss events
:return diameter_alg_hist <Histogram> - the PDV for the given .newick
:return elapsed <float> - the time it took to compute the PDV
None if time_it is False
"""
# From the newick tree create the reconciliation graph
edge_species_tree, edge_gene_tree, dtl_recon_graph, mpr_count, best_roots \
= DTLReconGraph.reconcile(tree_data, d, t, l)
# If we want to know the number of MPRs
#print(mpr_count)
# Reformat the host and parasite tree to use it with the histogram algorithm
gene_tree, gene_tree_root, gene_node_count = Diameter.reformat_tree(
edge_gene_tree, "pTop")
species_tree, species_tree_root, species_node_count \
= Diameter.reformat_tree(edge_species_tree, "hTop")
if time_it:
start = time.time()
# Calculate the histogram via histogram algorithm
diameter_alg_hist = HistogramAlg.diameter_algorithm(
species_tree, gene_tree, gene_tree_root, dtl_recon_graph,
dtl_recon_graph, False, zero_loss)
if time_it:
end = time.time()
elapsed = end - start
else:
elapsed = None
if normalize:
# Number of internal gene tree nodes
gene_tree_nodes = int(math.ceil(len(gene_tree) / 2.0))
diameter_alg_hist = diameter_alg_hist.xscale(1.0 /
(2 * gene_tree_nodes))
return diameter_alg_hist, elapsed
# Calculate the histogram via brute force
brute_force_hist = HistogramAlgTools.BF_find_histogram(
dtl_recon_graph, best_roots)
# Reformat the host and parasite tree to use it with the histogram algorithm
gene_tree, gene_tree_root, gene_node_count = Diameter.reformat_tree(
edge_gene_tree, "pTop")
species_tree, species_tree_root, species_node_count \
= Diameter.reformat_tree(edge_species_tree, "hTop")
# Calculate the histogram via histogram algorithm
diameter_alg_hist = HistogramAlg.diameter_algorithm(
species_tree,
gene_tree,
gene_tree_root,
dtl_recon_graph,
dtl_recon_graph,
False,
False,
verify=True)
# If there is a mismatch, print the details and save the tree that causes
# the error to a folder called errorTrees.
if brute_force_hist != diameter_alg_hist:
outname = './errorTrees/no%d-id%d-%d%d%d.png' % (
tree_size, tree_id, D, T, L)
ReconciliationVisualization.visualizeAndSave(
dtl_recon_graph, outname)
expected_n_pairs = HistogramAlgTools.calculate_n_pairs(
mpr_count)
brute_force_n_pairs = HistogramAlgTools.count_mpr_pairs(
def get_hist(g):
h = HistogramAlg.diameter_algorithm(species_tree, gene_tree, gene_root,
g, g, False, False)
return h.histogram_dict
def score(g):
hist = HistogramAlg.diameter_algorithm(species_tree, gene_tree,
gene_root, g, g, False, False)
return hist.mean()