ReconGraph Proposal

A proposal to change the old version of reconciliation graph dictionary to a class. The code for the data structures are in recon.py. The code to change the old version dict to the new ReconGraph or Reconciliation is in examples.py.

The documentation is in Read The Docs.

# Old dictionary structure
old_recon_graph = {
   ('n0', 'm2'): [('S', ('n2', 'm3'), ('n1', 'm4'))],
   ('n1', 'm4'): [('C', (None, None), (None, None))],
   ('n2', 'm3'): [('T', ('n3', 'm3'), ('n4', 'm1'))],
   ('n3', 'm3'): [('C', (None, None), (None, None))],
   ('n4', 'm1'): [('C', (None, None), (None, None))],
}

# New ReconGraph structure
source = MappingNode('n0', 'm2')
recongraph = ReconGraph(sources=[source])
recongraph.add_event(MappingNode('n0', 'm2'), Cospeciation(MappingNode('n2', 'm3'), MappingNode('n1', 'm4')))
recongraph.add_event(MappingNode('n1', 'm4'), TipTip())
recongraph.add_event(MappingNode('n2', 'm3'), Transfer(MappingNode('n3', 'm3'), MappingNode('n4', 'm1')))
recongraph.add_event(MappingNode('n3', 'm3'), TipTip())
recongraph.add_event(MappingNode('n4', 'm1'), TipTip())

# New (single) Reconciliation structure
source = MappingNode('n0', 'm2')
recon = Reconciliation(source)
recon.set_event(MappingNode('n0', 'm2'), Cospeciation(MappingNode('n2', 'm3'), MappingNode('n1', 'm4')))
recon.set_event(MappingNode('n1', 'm4'), TipTip())
recon.set_event(MappingNode('n2', 'm3'), Transfer(MappingNode('n3', 'm3'), MappingNode('n4', 'm1')))
recon.set_event(MappingNode('n3', 'm3'), TipTip())
recon.set_event(MappingNode('n4', 'm1'), TipTip())

# Convert old format to (single) Reconciliation
recongraph = converter.dict_to_recongraph(old_recon_graph)
print(recongraph)

# Convert old format to ReconGraph
recon = converter.dict_to_reconciliation(old_recon_graph)
print(recon)