def run(args):
from ete2 import Tree, PhyloTree
for nw in args.src_tree_iterator:
if args.orthologs is not None:
t = PhyloTree(nw)
for e in t.get_descendant_evol_events():
print e.in_seqs, e.out_seqs
def run(args):
from ete2 import Tree, PhyloTree
for nw in args.src_tree_iterator:
if args.orthologs is not None:
t = PhyloTree(nw)
for e in t.get_descendant_evol_events():
print e.in_seqs, e.out_seqs
# get tree files from directory
tree_files = os.listdir(str(sys.argv[1]))
for tree in tree_files:
if re.match(r"^\d+\.fna\.aln.+\.tree", tree):
# get orthogroup id
ortho = re.sub(r'\D', "", tree)
# load newick tree
#print(tree)
t = PhyloTree(tree)
#print(t)
evts = file('%s' '/' '%s' '.temp' % (events_dir, tree), "w")
##########################################################################################
# evolutionary events involving all taxa
##########################################################################################
# Alternatively, you can scan the whole tree topology
events = t.get_descendant_evol_events()
# print its orthology and paralogy relationships
for ev in events:
if ev.etype == "S":
evts.write(",".join(ev.in_seqs))
evts.write("<===>")
evts.write(",".join(ev.out_seqs))
evts.write("\n")
elif ev.etype == "D":
evts.write(",".join(ev.in_seqs))
evts.write("<===>")
evts.write(",".join(ev.out_seqs))
evts.write("\n")
evts.close()
##########################################################################################
# Get support value for the evolutionary events
# 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"
