def test_trim_tails_by_freq_forks(self):
g = DeBruijnGraph()
for s, t in itertools.combinations([1, 2, 3, 4, 5, 6], 2):
g.add_edge(s, t)
print('s => t', s, t)
g.add_edge(6, 1)
g.add_node(10) # singlet
g.add_edge(7, 6)
g.add_edge(8, 7)
g.add_edge(9, 8)
g.trim_tails_by_freq(2)
self.assertEqual([1, 2, 3, 4, 5, 6], sorted(g.nodes()))
g = DeBruijnGraph()
for s, t in itertools.combinations([1, 2, 3, 4, 5, 6], 2):
g.add_edge(s, t)
g.add_node(10) # singlet
g.add_edge(6, 1)
g.add_edge(7, 6)
g.add_edge(7, 8)
g.add_edge(8, 7)
g.add_edge(9, 8)
g.trim_tails_by_freq(2)
self.assertEqual([1, 2, 3, 4, 5, 6, 7, 8], sorted(g.nodes()))
g = DeBruijnGraph()
for s, t in itertools.combinations([1, 2, 3, 4, 5, 6], 2):
g.add_edge(s, t)
g.add_node(10) # singlet
g.add_edge(6, 1)
g.add_edge(7, 6)
g.add_edge(7, 8)
g.add_edge(9, 8)
g.trim_tails_by_freq(2)
self.assertEqual([1, 2, 3, 4, 5, 6], sorted(g.nodes()))
def test_add_edge(self):
g = DeBruijnGraph()
g.add_edge(1, 2)
self.assertEqual(1, g.get_edge_freq(1, 2))
g.add_edge(1, 2)
self.assertEqual(2, g.get_edge_freq(1, 2))
g.add_edge(1, 2, 5)
self.assertEqual(7, g.get_edge_freq(1, 2))
def test_add_edge(self):
g = DeBruijnGraph()
g.add_edge(1, 2)
assert g.get_edge_freq(1, 2) == 1
g.add_edge(1, 2)
assert g.get_edge_freq(1, 2) == 2
g.add_edge(1, 2, 5)
assert g.get_edge_freq(1, 2) == 7
def test_trim_noncutting_paths_by_freq_degree_stop(self):
g = DeBruijnGraph()
for s, t in itertools.combinations([1, 2, 3, 4], 2):
g.add_edge(s, t, freq=4)
for s, t in itertools.combinations([5, 6, 7, 8], 2):
g.add_edge(s, t, freq=4)
path1 = [5, 9, 10, 11, 12, 1]
for s, t in zip(path1, path1[1:]):
g.add_edge(s, t)
for edge in g.edges():
print(edge)
g.trim_noncutting_paths_by_freq(3)
print('g.nodes', g.nodes)
assert g.get_nodes() == list(range(1, 9)) + path1[1:-1]
print('g.nodes', g.nodes)
# add an equal weight path to force namesorting
path2 = [5, 13, 14, 15, 16, 1]
for s, t in zip(path2, path2[1:]):
g.add_edge(s, t)
print('g.nodes', g.nodes)
g.trim_noncutting_paths_by_freq(3)
print('g.nodes', g.nodes)
assert g.get_nodes() == list(range(1, 9)) + path2[1:-1]
# add back the original path with a higher (but still low) weight
for s, t in zip(path1, path1[1:]):
g.add_edge(s, t, freq=2)
g.trim_noncutting_paths_by_freq(3)
assert g.get_nodes() == list(range(1, 9)) + path1[1:-1]
# add the second path with 1 high weight edge
path2 = [5, 13, 14, 15, 16, 1]
for s, t in zip(path2, path2[1:]):
g.add_edge(s, t)
g.add_edge(14, 15, freq=6)
g.trim_noncutting_paths_by_freq(3)
assert g.get_nodes() == list(range(1, 9)) + path2[1:-1]