I may have found a way to go, but I'd like to know what I was doing wrong
before.
Now I don't create a new graph by union, but this (as vertex numbers and
indexes are the same):
gu = gt.Graph(directed=False)
gu.add_vertex(g_atac.num_vertices())
layer = gu.new_edge_property('int')
for e in g_rna.edges():
ne = gu.add_edge(e.source(), e.target())
layer[ne] = -1
for e in g_atac.edges():
ne = gu.add_edge(e.source(), e.target())
layer[ne] = 1
gu.ep['layer'] = layer
this works and the final graph has 2 layers and no extra zeros
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