def test_returns_two_nodes_in_order(self):
# given
b = CortexGraphBuilder()
b.with_colors(0)
b.add_path('AAA', 'AAT', 'ATA')
# when
graph = b.build()
# then
search = UnitigSearch.from_node_and_graph('AAA', graph)
assert ['AAT', 'ATA'] == list(
search.next_unitig_node_iter(EdgeTraversalOrientation.original))
search = UnitigSearch.from_node_and_graph('ATA', graph)
assert ['AAT', 'AAA'] == list(
search.next_unitig_node_iter(EdgeTraversalOrientation.reverse))
def test_two_connected_nodes_are_a_unitig(self, num_colors):
# given
colors = list(range(num_colors))
coverage = [1] + [0 for _ in range(1, num_colors)]
b = CortexGraphBuilder()
b.with_colors(*colors)
b.with_node_coverage('AAA', *coverage)
b.with_node_coverage('AAT', *coverage)
b.add_edge_with_color('AAA', 'AAT', 0)
# when
graph = b.build()
# then
search = UnitigSearch.from_node_and_graph('AAA', graph)
assert not search.is_unitig_end('AAA', EdgeTraversalOrientation.original)
assert search.is_unitig_end('AAA', EdgeTraversalOrientation.reverse)
search = UnitigSearch.from_node_and_graph('AAT', graph)
assert search.is_unitig_end('AAT', EdgeTraversalOrientation.original)
assert not search.is_unitig_end('AAT', EdgeTraversalOrientation.reverse)
def test_two_colors_to_one_color_is_node_end(self, start_node, orientation):
# given
b = CortexGraphBuilder()
b.with_colors(0, 1)
b.with_node_coverage('AAA', 1, 1)
b.with_node_coverage('AAT', 1, 0)
b.add_edge_with_color('AAA', 'AAT', 0)
# when
graph = b.build()
# then
search = UnitigSearch.from_node_and_graph(start_node, graph)
assert search.is_unitig_end(start_node, orientation)
def test_multi_color_y_graph_always_has_three_unitigs(self, data, num_colors, orientation):
# given
colors = list(range(num_colors))
edge_colors = [data.draw(s.sampled_from(colors)) for _ in range(3)]
b = CortexGraphBuilder()
b.with_colors(*colors)
for edge_color in edge_colors:
b.add_edge_with_color_and_coverage('AAA', 'AAT', edge_color, color_coverage=1)
b.add_edge_with_color_and_coverage('AAT', 'ATA', edge_colors[1], color_coverage=1)
b.add_edge_with_color_and_coverage('AAT', 'ATC', edge_colors[2], color_coverage=1)
# when
graph = b.build()
# then
for node in ['ATA', 'ATC']:
search = UnitigSearch.from_node_and_graph(node, graph)
search.is_unitig_end(node, orientation)
search = UnitigSearch.from_node_and_graph('AAA', graph)
assert not search.is_unitig_end('AAA', EdgeTraversalOrientation.original)
assert search.is_unitig_end('AAA', EdgeTraversalOrientation.reverse)
assert search.is_unitig_end('AAT', EdgeTraversalOrientation.original)
assert not search.is_unitig_end('AAT', EdgeTraversalOrientation.reverse)
def test_middle_unconnected_node_for_one_color_in_two_color_graph_results_in_three_unitigs(
self, start_node, orientation
):
# given
b = CortexGraphBuilder()
b.with_colors(0, 1)
b.with_node_coverage('AAA', 1, 1)
b.with_node_coverage('AAT', 1, 1)
b.with_node_coverage('ATA', 1, 1)
b.add_edge_with_color('AAA', 'AAT', 0)
b.add_edge_with_color('AAT', 'ATA', 0)
# when
graph = b.build()
search = UnitigSearch.from_node_and_graph(start_node, graph)
assert search.is_unitig_end(start_node, orientation)
def test_two_colors_to_two_nodes_in_first_color_is_node_end(self):
# given
b = CortexGraphBuilder()
b.with_colors(0, 1)
b.with_node_coverage('AAA', 1, 1)
b.with_node_coverage('AAT', 1, 0)
b.with_node_coverage('AAC', 1, 0)
b.add_edge_with_color('AAA', 'AAT', 0)
b.add_edge_with_color('AAA', 'AAC', 0)
# when
graph = b.build()
# then
for orientation in EdgeTraversalOrientation:
for node in ['AAA', 'AAT', 'AAC']:
search = UnitigSearch.from_node_and_graph(node, graph)
assert search.is_unitig_end(node, orientation)