def test_path_graph_factory():
t_dict, locus = read_single_locus('path1.gtf')
sgraph = SpliceGraph.create(t_dict.values())
pgraphfactory = PathGraphFactory(sgraph)
g1 = pgraphfactory.create(k=1)
assert len(g1) == 5
g2 = pgraphfactory.create(k=2)
assert len(g2) == 6
gopt, k = pgraphfactory.create_optimal()
assert k == 2
return
def test_path1():
t_dict, locus = read_single_locus('path1.gtf')
transfrags = locus.get_transfrags(Strand.POS)
sgraph = SpliceGraph.create(transfrags)
k = 2
pgf = PathGraphFactory(sgraph)
pgraph = pgf.create(k)
paths = find_paths(pgraph)
return
def test_topological_sort():
G = Graph()
G.add_path((G.SOURCE, 10, 20, 30, 40, G.SINK))
G.add_path((G.SOURCE, 10, 30, 40, G.SINK))
G.add_path((G.SOURCE, 10, G.SINK))
G.add_path((G.SOURCE, 20, G.SINK))
assert G.is_topological_sort(G.topological_sort())
t_dict, locus = read_single_locus('noc2l_locus.gtf')
for sgraph in locus.create_splice_graphs():
pgf = PathGraphFactory(sgraph)
G = pgf.create(k=1)
assert G.is_topological_sort(G.topological_sort())
assert G.is_topological_sort(G.topological_sort_dfs())
