def draw_events_tree(tree, stree, gene2species, **options):
phylo.init_dup_loss_tree(stree)
phylo.count_dup_loss_tree(tree, stree, gene2species)
phylo.count_ancestral_genes(stree)
labels = options.get("labels", {})
for node in stree:
labels[node.name] = ""
if node.data['dup'] > 0:
labels[node.name] += " +%d" % node.data['dup']
else:
labels[node.name] += " "
if node.data['loss'] > 0:
labels[node.name] += " -%d" % node.data['loss']
else:
labels[node.name] += " "
if labels[node.name] != "":
labels[node.name] += ": "
labels[node.name] += "%d" % node.data['genes']
draw_tree(stree, labels=labels, **options)
def draw_events_tree(tree, stree, gene2species, **options):
phylo.init_dup_loss_tree(stree)
phylo.count_dup_loss_tree(tree, stree, gene2species)
phylo.count_ancestral_genes(stree)
labels = options.get("labels", {})
for node in stree:
labels[node.name] = ""
if node.data['dup'] > 0:
labels[node.name] += " +%d" % node.data['dup']
else:
labels[node.name] += " "
if node.data['loss'] > 0:
labels[node.name] += " -%d" % node.data['loss']
else:
labels[node.name] += " "
if labels[node.name] != "":
labels[node.name] += ": "
labels[node.name] += "%d" % node.data['genes']
draw_tree(stree, labels=labels, **options)
def process_tree(tree, stree, gene2species):
#==============================
# process
if options.hist or options.hashes:
# count topology
hashes.append(phylo.hash_tree(tree, gene2species))
elif options.histsplit:
# count splits
for leaf in tree.leaves():
tree.rename(leaf.name, gene2species(leaf.name))
splits.extend(phylo.find_splits(tree))
elif options.dump:
# dump mode
dump_tree(tree)
elif options.events:
# add event labels
assert stree is not None and gene2species is not None
phylo.count_dup_loss_tree(tree, stree, gene2species)
else:
# default mode: display tree
display_tree(tree, options, gene2species=gene2species, stree=stree)
def process_tree(tree, stree, gene2species):
#==============================
# process
if options.hist or options.hashes:
# count topology
hashes.append(phylo.hash_tree(tree, gene2species))
elif options.histsplit:
# count splits
for leaf in tree.leaves():
tree.rename(leaf.name, gene2species(leaf.name))
splits.extend(phylo.find_splits(tree))
elif options.dump:
# dump mode
dump_tree(tree)
elif options.events:
# add event labels
assert stree is not None and gene2species is not None
phylo.count_dup_loss_tree(tree, stree, gene2species)
else:
# default mode: display tree
display_tree(tree, options, gene2species=gene2species, stree=stree)
def count_dup_loss_coal_tree(coal_tree, extra, stree, gene2species,
implied=True, locus_mpr=True):
"""count dup loss coal"""
if not locus_mpr:
raise Exception("not implemented")
# TODO: use locus_recon and locus_events rather than MPR
# (currently, phylo.py reconciliation functions fail for non-MPR)
locus_tree = extra["locus_tree"]
locus_recon = phylo.reconcile(locus_tree, stree, gene2species)
locus_events = phylo.label_events(locus_tree, locus_recon)
coal_recon = extra["coal_recon"]
ndup, nloss, nappear = phylo.count_dup_loss_tree(locus_tree, stree, gene2species,
locus_recon, locus_events)
# add implied speciation nodes if desired
# this must be added AFTER counting dups and losses since it affects loss inference
if implied:
added = phylo.add_implied_spec_nodes(locus_tree, stree, locus_recon, locus_events)
# count coals
ncoal = 0
counts = coal.count_lineages_per_branch(coal_tree, coal_recon, locus_tree)
for lnode, (count_bot, count_top) in counts.iteritems():
n = max(count_top-1, 0)
locus_recon[lnode].data['coal'] += n
ncoal += n
if implied:
phylo.remove_implied_spec_nodes(locus_tree, added, locus_recon, locus_events)
return ndup, nloss, ncoal, nappear
def count_dup_loss_coal_tree(coal_tree,
extra,
stree,
gene2species,
implied=True,
locus_mpr=True):
"""count dup loss coal"""
if not locus_mpr:
raise Exception("not implemented")
# TODO: use locus_recon and locus_events rather than MPR
# (currently, phylo.py reconciliation functions fail for non-MPR)
locus_tree = extra["locus_tree"]
locus_recon = phylo.reconcile(locus_tree, stree, gene2species)
locus_events = phylo.label_events(locus_tree, locus_recon)
coal_recon = extra["coal_recon"]
ndup, nloss, nappear = phylo.count_dup_loss_tree(locus_tree, stree,
gene2species, locus_recon,
locus_events)
# add implied speciation nodes if desired
# this must be added AFTER counting dups and losses since it affects loss inference
if implied:
added = phylo.add_implied_spec_nodes(locus_tree, stree, locus_recon,
locus_events)
# count coals
ncoal = 0
counts = coal.count_lineages_per_branch(coal_tree, coal_recon, locus_tree)
for lnode, (count_bot, count_top) in counts.iteritems():
n = max(count_top - 1, 0)
locus_recon[lnode].data['coal'] += n
ncoal += n
if implied:
phylo.remove_implied_spec_nodes(locus_tree, added, locus_recon,
locus_events)
return ndup, nloss, ncoal, nappear