def get_orthology_graph( t,seedname,phyid ):
"""Return graph representing orthology relationships from the tree."""
#get evol_events
evolEvents,seednode=get_evolEvents( t,phyid,seedname )
if not evolEvents:
return
#create orthologs graph
ortho_graph=MyGraph( t.get_leaf_names() ) #non-directed graph
#populate it with orthologs
for e in filter( lambda x: x.etype=='S',evolEvents ): #seednode.get_my_evol_events() ):
for o1 in e.out_seqs:
for o2 in e.in_seqs:
ortho_graph.add_line( o1,o2 )
return ortho_graph
def get_orthology_graph(t, seedname, phyid):
"""Return graph representing orthology relationships from the tree."""
#get evol_events
evolEvents, seednode = get_evolEvents(t, phyid, seedname)
if not evolEvents:
return
#create orthologs graph
ortho_graph = MyGraph(t.get_leaf_names()) #non-directed graph
#populate it with orthologs
for e in filter(lambda x: x.etype == 'S',
evolEvents): #seednode.get_my_evol_events() ):
for o1 in e.out_seqs:
for o2 in e.in_seqs:
ortho_graph.add_line(o1, o2)
return ortho_graph
def populate_orthology_graph( t,seedname,phyid,species_list ):
#get seed orthologs
orthologs=get_orthologs( t,seedname,phyid,species_list )
if not orthologs:
return [],None
#create orthologs graph
ortho_graph=MyGraph( orthologs ) #non-directed graph
#populate it with orthologs
for orth in orthologs:
if orth==seedname:
continue
ortho_graph.add_line( seedname, orth )
#mark all orthologs of given ortholog in the graph
for orth_in in get_orthologs( t,orth,phyid,species_list ):
if orth_in in orthologs:
ortho_graph.add_line( orth, orth_in )
return orthologs,ortho_graph
def populate_orthology_graph( t,seedname,phyid,species_list ):
#get seed orthologs
orthologs=get_orthologs( t,seedname,phyid,species_list )
if not orthologs:
return [],None
#create orthologs graph
ortho_graph=MyGraph( orthologs ) #non-directed graph
#populate it with orthologs
for orth in orthologs:
if orth==seedname:
continue
ortho_graph.add_line( seedname, orth )
#mark all orthologs of given ortholog in the graph
for orth_in in get_orthologs( t,orth,phyid,species_list ):
if orth_in in orthologs:
ortho_graph.add_line( orth, orth_in )
return orthologs,ortho_graph
