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from ete3 import PhyloTree
# Loads an example tree
nw = """
((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),
(Ptr_002,(Hsa_002,Mmu_002))));
"""
t = PhyloTree(nw)
print(t)
# /-Dme_001
# /--------|
# | \-Dme_002
# |
# | /-Cfa_001
# | /--------|
#---------| | \-Mms_001
# | /--------|
# | | | /-Hsa_001
# | | | /--------|
# | | \--------| \-Ptr_001
# \--------| |
# | \-Mmu_001
# |
# | /-Ptr_002
# \--------|
# | /-Hsa_002
# \--------|
# \-Mmu_002
#
# To obtain all the evolutionary events involving a given leaf node we
# use get_my_evol_events method
matches = t.search_nodes(name="Hsa_001")
human_seq = matches[0]
# Obtains its evolutionary events
events = human_seq.get_my_evol_events()
# Print its orthology and paralogy relationships
print("Events detected that involve Hsa_001:")
for ev in events:
if ev.etype == "S":
print(' ORTHOLOGY RELATIONSHIP:', ','.join(ev.in_seqs), "<====>", ','.join(ev.out_seqs))
elif ev.etype == "D":
print(' PARALOGY RELATIONSHIP:', ','.join(ev.in_seqs), "<====>", ','.join(ev.out_seqs))
# Alternatively, you can scan the whole tree topology
events = t.get_descendant_evol_events()
# Print its orthology and paralogy relationships
print("Events detected from the root of the tree")
for ev in events:
if ev.etype == "S":
print(' ORTHOLOGY RELATIONSHIP:', ','.join(ev.in_seqs), "<====>", ','.join(ev.out_seqs))
elif ev.etype == "D":
print(' PARALOGY RELATIONSHIP:', ','.join(ev.in_seqs), "<====>", ','.join(ev.out_seqs))
# If we are only interested in the orthology and paralogy relationship
# among a given set of species, we can filter the list of sequences
#
# fseqs is a function that, given a list of sequences, returns only
# those from human and mouse
fseqs = lambda slist: [s for s in slist if s.startswith("Hsa") or s.startswith("Mms")]
print("Paralogy relationships among human and mouse")
for ev in events:
if ev.etype == "D":
# Prints paralogy relationships considering only human and
# mouse. Some duplication event may not involve such species,
# so they will be empty
print(' PARALOGY RELATIONSHIP:', \
','.join(fseqs(ev.in_seqs)), \
"<====>",\
','.join(fseqs(ev.out_seqs)))
# Note that besides the list of events returned, the detection
# algorithm has labeled the tree nodes according with the
# predictions. We can use such lables as normal node features.
dups = t.search_nodes(evoltype="D") # Return all duplication nodes
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