def observed_edges_from_gene_multiset(gene_multiset):
obverse_edges = set()
for gene, copies in gene_multiset.items():
for i in range(1, copies + 1):
obverse_edges.add((get_extremity_by_gene(gene, True, i),
get_extremity_by_gene(gene, False, i)))
return obverse_edges
def define_equiv_function(gene_multiset, vertex2ind, bar_vertex2ind):
equiv = {}
for gene, copies in gene_multiset.items():
for left in [True, False]:
temp = []
for i in range(1, copies + 1):
temp.append(bar_vertex2ind[get_extremity_by_gene(gene, left, i)])
equiv[vertex2ind[get_extremity_by_gene(gene, left, 1)]] = temp
return equiv
def vertex_set_from_gene_multiset(gene_multiset):
vertex_set = set()
for gene, copies in gene_multiset.items():
for left in [True, False]:
for i in range(1, copies + 1):
vertex_set.add(get_extremity_by_gene(gene, left, i))
return vertex_set
def get_genome_graph_from_vars(rs, r_dot, gene_set, edge_set, telomer_set, ind2vertex):
result_graph = bg.breakpoint_graph.BreakpointGraph()
# graph = nx.Graph()
#
# for gene in gene_set:
# graph.add_node(get_extremity_by_gene(gene, True, 1)[:-2])
# graph.add_node(get_extremity_by_gene(gene, False, 1)[:-2])
name2vertices = {}
for gene in gene_set:
left, right = bg.vertices.TaggedBlockVertex(get_extremity_by_gene(gene, True, 1)[:-2]), \
bg.vertices.TaggedBlockVertex(get_extremity_by_gene(gene, False, 1)[:-2])
left.mate_vertex = right
right.mate_vertex = left
name2vertices[left.name] = left
name2vertices[right.name] = right
# text_multiset = defaultdict(list)
# text_set = set()
# for u, v in edge_set:
# i, j = tuple(sorted([u, v]))
# if rs[i, j].x == 1:
# if ind2vertex[j][:-2] == ind2vertex[i][:-2]:
# print("ALLERT ALLERT")
# text_multiset[ind2vertex[i][:-2]].append(ind2vertex[j][:-2])
# text_multiset[ind2vertex[j][:-2]].append(ind2vertex[i][:-2])
# text_set.add(ind2vertex[i][:-2])
# text_set.add(ind2vertex[j][:-2])
# graph.add_edge(ind2vertex[i][:-2], ind2vertex[j][:-2])
# for a, b in text_multiset.items():
# if len(b) != 1:
# print(a)
# print(b)
# text_set2 = set()
# for u, cond in telomer_set.items():
# if cond and r_dot[u].x == 1:
# text_set2.add(ind2vertex[u][:-2])
# if ind2vertex[u][:-2] in text_set:
# print("ALERT! ALERT! ALERT!")
# graph.add_node(ind2vertex[u][:-2])
#
# print("----MISSING-----")
# for v in graph:
# if len(list(graph.neighbors(v))) == 0:
# if v not in text_set2:
# print("Alert!")
# print(v)
for u, v in edge_set:
i, j = tuple(sorted([u, v]))
if rs[i, j].x == 1:
result_graph.add_edge(name2vertices[ind2vertex[i][:-2]],
name2vertices[ind2vertex[j][:-2]],
bg.multicolor.Multicolor(1), merge=False)
for u, cond in telomer_set.items():
if cond and r_dot[u].x == 1:
result_graph.add_edge(name2vertices[ind2vertex[u][:-2]],
bg.vertices.TaggedInfinityVertex(ind2vertex[u][:-2]),
bg.multicolor.Multicolor(1), merge=False)
return result_graph.get_blocks_order()