def test_edges_are_consistent(self):
'''test edges_are_consistent'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertTrue(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 100, 50, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 42, 1))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertFalse(self.g._edges_are_consistent('c1', 'c2', 'c3'))
def test_remove_redundant_nodes_from_simple_path(self):
'''test remove_redundant_nodes_from_simple_path'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 100, 142, 'c3', 1, 42))
new_path = self.g.remove_redundant_nodes_from_simple_path(
['c1', 'c2', 'c3'])
self.assertListEqual(['c1', 'c2', 'c3'], new_path)
self.assertTrue('c2' in self.g.graph)
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 51, 100, 'c2', 1, 50))
self.g.add_edge(edge.Edge('c2', 41, 80, 'c3', 1, 40))
new_path = self.g.remove_redundant_nodes_from_simple_path(
['c1', 'c2', 'c3'])
self.assertListEqual(['c1', 'c3'], new_path)
self.assertFalse('c2' in self.g.graph)
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 51, 100, 'c2', 1, 50))
self.g.add_edge(edge.Edge('c2', 41, 80, 'c3', 1, 40))
self.g.add_edge(edge.Edge('c3', 100, 150, 'c4', 1, 50))
self.g.add_edge(edge.Edge('c4', 20, 70, 'c5', 1, 50))
self.g.add_edge(edge.Edge('c5', 40, 90, 'c6', 1, 50))
new_path = self.g.remove_redundant_nodes_from_simple_path(
['c1', 'c2', 'c3', 'c4', 'c5', 'c6'])
self.assertListEqual(['c1', 'c3', 'c5', 'c6'], new_path)
self.assertFalse('c2' in self.g.graph)
self.assertFalse('c4' in self.g.graph)
def test_node_to_coords(self):
'''test _node_to_coords'''
self.g.add_edge(edge.Edge('c1', 199, 0, 'c2', 1319, 1119))
nodes = ['c1', 'c2']
self.assertListEqual(['c1', intervals.Interval(200, 659), True], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(0, 1319), True], self.g._node_to_coords(nodes, 1))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c2', 1119, 1319, 'c1', 0, 199))
nodes = ['c1', 'c2']
self.assertListEqual(['c1', intervals.Interval(200, 659), True], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(0, 1319), True], self.g._node_to_coords(nodes, 1))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 551, 650, 'c2', 1, 100))
self.g.add_edge(edge.Edge('c2', 1201, 1300, 'c3', 11, 110))
nodes = ['c1', 'c2', 'c3']
self.assertListEqual(['c1', intervals.Interval(0, 550), False], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(1, 1200), False], self.g._node_to_coords(nodes, 1))
self.assertListEqual(['c3', intervals.Interval(11, 2159), False], self.g._node_to_coords(nodes, 2))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 551, 650, 'c2', 1, 100))
self.g.add_edge(edge.Edge('c3', 110, 11, 'c2', 1300, 1201))
self.g.add_edge(edge.Edge('c3', 2051, 2150, 'c4', 6, 115))
nodes = ['c1', 'c2', 'c3', 'c4']
self.assertListEqual(['c1', intervals.Interval(0, 550), False], self.g._node_to_coords(nodes, 0))
self.assertListEqual(['c2', intervals.Interval(1, 1200), False], self.g._node_to_coords(nodes, 1))
self.assertListEqual(['c3', intervals.Interval(11, 2050), False], self.g._node_to_coords(nodes, 2))
self.assertListEqual(['c4', intervals.Interval(6, 1259), False], self.g._node_to_coords(nodes, 3))
def test_simple_path_is_consistent(self):
'''test simple_path_is_consistent'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertTrue(self.g.simple_path_is_consistent(['c1', 'c2']))
self.g.add_edge(edge.Edge('c3', 10, 100, 'c4', 1, 1000))
self.assertTrue(self.g.simple_path_is_consistent(['c1', 'c2', 'c3']))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 1000, 100, 'c3', 1, 42))
self.assertFalse(self.g.simple_path_is_consistent(['c1', 'c2', 'c3']))
def test_remove_middle_node(self):
'''test remove_middle_node'''
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 100, 142, 'c3', 1, 42))
self.assertFalse(self.g._remove_middle_node('c1', 'c2', 'c3'))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 51, 100, 'c2', 1, 50))
self.g.add_edge(edge.Edge('c2', 41, 80, 'c3', 1, 40))
self.assertTrue(self.g._remove_middle_node('c1', 'c2', 'c3'))
self.assertTrue('c2' not in self.g.graph)
self.assertEqual(1, len(self.g.graph['c1']['c3']['edges']))
self.assertEqual(1, len(self.g.graph['c3']['c1']['edges']))
self.assertEqual(self.g.graph['c1']['c3']['edges'][0], edge.Edge('c1', 91, 100, 'c3', 1, 10))
self.assertEqual(self.g.graph['c3']['c1']['edges'][0], edge.Edge('c1', 91, 100, 'c3', 1, 10))
def test_find_simple_path(self):
'''test find_simple_path'''
self.assertListEqual([], self.g.find_simple_path(['c1']))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.assertListEqual(['c1', 'c2'], self.g.find_simple_path(['c1', 'c2']))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertListEqual(['c1', 'c2', 'c3'], self.g.find_simple_path(['c1', 'c2', 'c3']))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.assertListEqual([], self.g.find_simple_path(['c1', 'c2', 'c3']))
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.assertListEqual([], self.g.find_simple_path(['c1', 'c2']))
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 1, 100, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 50, 100, 'c3', 1, 42))
self.g.add_edge(edge.Edge('c3', 10, 100, 'c4', 1, 1000))
self.assertListEqual(['c1', 'c2', 'c3', 'c4'], self.g.find_simple_path(['c1', 'c2', 'c3', 'c4']))
self.g.add_edge(edge.Edge('c3', 10, 100, 'c5', 1, 1000))
self.assertListEqual([], self.g.find_simple_path(['c1', 'c2', 'c3']))
def test_merged_coords_from_simple_nonredundant_path(self):
'''test merged_coords_from_simple_nonredundant_path'''
self.g.add_edge(edge.Edge('c1', 199, 0, 'c2', 1319, 1119))
nodes = ['c1', 'c2']
coords = self.g.merged_coords_from_simple_nonredundant_path(nodes)
expected = [
['c1', intervals.Interval(200, 659), True],
['c2', intervals.Interval(0, 1319), True],
]
self.assertListEqual(expected, coords)
self.g = graph.Graph(self.asm)
self.g.add_edge(edge.Edge('c1', 610, 652, 'c2', 1, 42))
self.g.add_edge(edge.Edge('c2', 1250, 1310, 'c3', 5, 65))
nodes = ['c1', 'c2', 'c3']
coords = self.g.merged_coords_from_simple_nonredundant_path(nodes)
expected = [['c1', intervals.Interval(0, 609), False],
['c2', intervals.Interval(1, 1249), False],
['c3', intervals.Interval(5, 2159), False]]
self.assertListEqual(expected, coords)
def _merge_overlapping_contigs(self, contigs):
if len(contigs) <= 1:
return
hits = self._run_nucmer(contigs)
assembly_graph = graph.Graph(self, contigs=contigs)
for hit in hits:
e = hit.to_graph_edge()
if e is not None:
assembly_graph.add_edge(e)
for connected_component in assembly_graph.connected_components():
if len(connected_component) < 2:
continue
simple_path = assembly_graph.find_simple_path(connected_component)
assert assembly_graph.simple_path_is_consistent(simple_path)
if len(simple_path) > 1:
simple_path = assembly_graph.remove_redundant_nodes_from_simple_path(simple_path)
coords = assembly_graph.merged_coords_from_simple_nonredundant_path(simple_path)
new_contig = self._coords_to_new_contig(coords)
for name, x, y in coords:
self._remove_contig(name)
self._add_contig(new_contig)
def setUp(self):
self.asm = assembly.Assembly(
contigs_file=os.path.join(data_dir, 'graph_test.contigs.fa'))
self.g = graph.Graph(self.asm)