def get_evol_events_from_leaf(node, sos_thr=0.0):
""" Returns a list of duplication and speciation events in
which the current node has been involved. Scanned nodes are
also labeled internally as dup=True|False. You can access this
labels using the 'node.dup' sintaxis.
Method: the algorithm scans all nodes from the given leafName to
the root. Nodes are assumed to be duplications when a species
overlap is found between its child linages. Method is described
more detail in:
"The Human Phylome." Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon
T. Genome Biol. 2007;8(6):R109.
"""
# Get the tree's root
root = node.get_tree_root()
# Checks that is actually rooted
outgroups = root.get_children()
if len(outgroups) != 2:
raise TypeError, "Tree is not rooted"
# Cautch the smaller outgroup (will be stored as the tree
# outgroup)
o1 = set([n.name for n in outgroups[0].get_leaves()])
o2 = set([n.name for n in outgroups[1].get_leaves()])
if len(o2)<len(o1):
smaller_outg = outgroups[1]
else:
smaller_outg = outgroups[0]
# Prepare to browse tree from leaf to root
all_events = []
current = node
ref_spcs = node.species
sister_leaves = set([])
browsed_spcs = set([current.species])
browsed_leaves = set([current])
# get family Size
fSize = len([n for n in root.get_leaves() if n.species == ref_spcs])
# Clean previous analysis
for n in root.get_descendants()+[root]:
n.del_feature("evoltype")
while current.up:
# distances control (0.0 distance check)
d = 0
for s in current.get_sisters():
for leaf in s.get_leaves():
d += current.get_distance(leaf)
sister_leaves.add(leaf)
# Process sister node only if there is any new sequence.
# (previene dupliaciones por nombres repetidos)
sister_leaves = sister_leaves.difference(browsed_leaves)
if len(sister_leaves)==0:
current = current.up
continue
# Gets species at both sides of event
sister_spcs = set([n.species for n in sister_leaves])
overlaped_spces = browsed_spcs & sister_spcs
all_spcs = browsed_spcs | sister_spcs
score = float(len(overlaped_spces))/len(all_spcs)
# Creates a new evolEvent
event = EvolEvent()
event.fam_size = fSize
event.seed = node.name
# event.e_newick = current.up.get_newick() # high mem usage!!
event.sos = score
event.outgroup = smaller_outg.name
# event.allseqs = set(current.up.get_leaf_names())
event.in_seqs = set([n.name for n in browsed_leaves])
event.out_seqs = set([n.name for n in sister_leaves])
event.inparalogs = set([n.name for n in browsed_leaves if n.species == ref_spcs])
# If species overlap: duplication
if score >sos_thr and d > 0.0:
event.node = current.up
event.etype = "D"
event.outparalogs = set([n.name for n in sister_leaves if n.species == ref_spcs])
event.orthologs = set([])
current.up.add_feature("evoltype","D")
all_events.append(event)
# If NO species overlap: speciation
elif score == sos_thr:
event.node = current.up
event.etype = "S"
event.orthologs = set([n.name for n in sister_leaves if n.species != ref_spcs])
event.outparalogs = set([])
current.up.add_feature("evoltype","S")
all_events.append(event)
else:
pass # do not add event if distances == 0
# Updates browsed species
browsed_spcs |= sister_spcs
browsed_leaves |= sister_leaves
sister_leaves = set([])
# And keep ascending
current = current.up
return all_events
def get_evol_events_from_leaf(node, sos_thr=0.0):
""" Returns a list of duplication and speciation events in
which the current node has been involved. Scanned nodes are
also labeled internally as dup=True|False. You can access this
labels using the 'node.dup' sintaxis.
Method: the algorithm scans all nodes from the given leafName to
the root. Nodes are assumed to be duplications when a species
overlap is found between its child linages. Method is described
more detail in:
"The Human Phylome." Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon
T. Genome Biol. 2007;8(6):R109.
"""
# Get the tree's root
root = node.get_tree_root()
# Checks that is actually rooted
outgroups = root.get_children()
if len(outgroups) != 2:
raise TypeError, "Tree is not rooted"
# Cautch the smaller outgroup (will be stored as the tree
# outgroup)
o1 = set([n.name for n in outgroups[0].get_leaves()])
o2 = set([n.name for n in outgroups[1].get_leaves()])
if len(o2) < len(o1):
smaller_outg = outgroups[1]
else:
smaller_outg = outgroups[0]
# Prepare to browse tree from leaf to root
all_events = []
current = node
ref_spcs = node.species
sister_leaves = set([])
browsed_spcs = set([current.species])
browsed_leaves = set([current])
# get family Size
fSize = len([n for n in root.get_leaves() if n.species == ref_spcs])
# Clean previous analysis
for n in root.get_descendants() + [root]:
n.del_feature("evoltype")
while current.up:
# distances control (0.0 distance check)
d = 0
for s in current.get_sisters():
for leaf in s.get_leaves():
d += current.get_distance(leaf)
sister_leaves.add(leaf)
# Process sister node only if there is any new sequence.
# (previene dupliaciones por nombres repetidos)
sister_leaves = sister_leaves.difference(browsed_leaves)
if len(sister_leaves) == 0:
current = current.up
continue
# Gets species at both sides of event
sister_spcs = set([n.species for n in sister_leaves])
overlaped_spces = browsed_spcs & sister_spcs
all_spcs = browsed_spcs | sister_spcs
score = float(len(overlaped_spces)) / len(all_spcs)
# Creates a new evolEvent
event = EvolEvent()
event.fam_size = fSize
event.seed = node.name
# event.e_newick = current.up.get_newick() # high mem usage!!
event.sos = score
event.outgroup = smaller_outg.name
# event.allseqs = set(current.up.get_leaf_names())
event.in_seqs = set([n.name for n in browsed_leaves])
event.out_seqs = set([n.name for n in sister_leaves])
event.inparalogs = set(
[n.name for n in browsed_leaves if n.species == ref_spcs])
# If species overlap: duplication
if score > sos_thr: # and d > 0.0: Removed branch control.
event.node = current.up
event.etype = "D"
event.outparalogs = set(
[n.name for n in sister_leaves if n.species == ref_spcs])
event.orthologs = set([])
current.up.add_feature("evoltype", "D")
all_events.append(event)
# If NO species overlap: speciation
elif score == sos_thr:
event.node = current.up
event.etype = "S"
event.orthologs = set(
[n.name for n in sister_leaves if n.species != ref_spcs])
event.outparalogs = set([])
current.up.add_feature("evoltype", "S")
all_events.append(event)
else:
pass # do not add event if distances == 0
# Updates browsed species
browsed_spcs |= sister_spcs
browsed_leaves |= sister_leaves
sister_leaves = set([])
# And keep ascending
current = current.up
return all_events
