def simple_test():
graph = Graph({
1: Block(10),
2: Block(1),
3: Block(1),
4: Block(10)
}, {
1: [2, 3],
2: [4],
3: [4]
})
graph.convert_to_numpy_backend()
sequence_graph = SequenceGraph.create_empty_from_ob_graph(graph)
sequence_graph.set_sequence(1, "GGGTTTATAC")
sequence_graph.set_sequence(2, "A")
sequence_graph.set_sequence(3, "C")
sequence_graph.set_sequence(4, "GTACATTGTA")
linear_ref = Interval(0, 10, [1, 2, 3], graph)
linear_ref = linear_ref.to_numpy_indexed_interval()
critical_nodes = set([4])
finder = MinimizerFinder(graph,
sequence_graph,
critical_nodes,
linear_ref,
k=3,
w=3)
minimizers = finder.find_minimizers()
assert minimizers.has_minimizer(2, 0)
assert minimizers.has_minimizer(3, 0)
assert minimizers.has_minimizer(4, 4)
def test_reverse():
graph = Graph({
1: Block(10),
2: Block(5),
3: Block(10),
4: Block(5)
}, {
1: [2, 3],
2: [4],
3: [4]
})
graph.convert_to_numpy_backend()
linear_path = NumpyIndexedInterval.from_interval(
Interval(0, 10, [1, 2, 4], graph))
alignments = [Interval(4, 5, [-3, -1], graph)]
projected = project_alignments(alignments, linear_path)
projected = list(projected)
assert projected[0] == (5, 16, "-")
def test_many_nodes():
nodes = {i: Block(1) for i in range(2, 10)}
nodes[1] = Block(10)
nodes[10] = Block(10)
graph = Graph(
nodes, {
1: [2, 3],
2: [4],
3: [4],
4: [5, 6],
5: [7],
6: [7],
7: [8, 9],
8: [10],
9: [10]
})
graph.convert_to_numpy_backend()
sequence_graph = SequenceGraph.create_empty_from_ob_graph(graph)
sequence_graph.set_sequence(1, "ACTGACTGAC")
sequence_graph.set_sequence(10, "ACTGACTGAC")
sequence_graph.set_sequence(2, "A")
sequence_graph.set_sequence(3, "C")
sequence_graph.set_sequence(4, "A")
sequence_graph.set_sequence(5, "G")
sequence_graph.set_sequence(6, "C")
sequence_graph.set_sequence(7, "T")
sequence_graph.set_sequence(8, "A")
sequence_graph.set_sequence(9, "A")
linear_ref = Interval(0, 10, [1, 2, 4, 6, 7, 8, 10], graph)
linear_ref = linear_ref.to_numpy_indexed_interval()
critical_nodes = {1, 4, 7, 10}
finder = MinimizerFinder(graph,
sequence_graph,
critical_nodes,
linear_ref,
k=3,
w=3)
minimizers = finder.find_minimizers()
print(len(minimizers.minimizers))
def test_simple():
graph = Graph({
1: Block(10),
2: Block(5),
3: Block(10),
4: Block(5)
}, {
1: [2, 3],
2: [4],
3: [4]
})
graph.convert_to_numpy_backend()
linear_path = NumpyIndexedInterval.from_interval(
Interval(0, 10, [1, 2, 4], graph))
alignments = [Interval(5, 5, [1, 3], graph), Interval(5, 5, [3, 4], graph)]
projected = project_alignments(alignments, linear_path)
projected = list(projected)
assert projected[0] == (5, 15, "+")
assert projected[1] == (15, 25, "+")
def test_many_nodes():
nodes = {i: Block(1) for i in range(2, 10)}
nodes[1] = Block(10)
nodes[10] = Block(10)
graph = Graph(
nodes, {
1: [2, 3],
2: [4],
3: [4],
4: [5, 6],
5: [7],
6: [7],
7: [8, 9],
8: [10],
9: [10]
})
graph.convert_to_numpy_backend()
sequence_graph = SequenceGraph.create_empty_from_ob_graph(graph)
sequence_graph.set_sequence(1, "ACTGACTGAC")
sequence_graph.set_sequence(10, "ACTGACTGAC")
sequence_graph.set_sequence(2, "A")
sequence_graph.set_sequence(3, "C")
sequence_graph.set_sequence(4, "A")
sequence_graph.set_sequence(5, "G")
sequence_graph.set_sequence(6, "C")
sequence_graph.set_sequence(7, "T")
sequence_graph.set_sequence(8, "T")
sequence_graph.set_sequence(9, "A")
linear_ref_nodes = {1, 2, 4, 6, 7, 8, 10}
read_sequence = "ACTGACCAGTAACTGAC"
start_node = 1
start_offset = 4
aligner = LocalGraphAligner(graph, sequence_graph, read_sequence,
linear_ref_nodes, start_node, start_offset)
alignment, score = aligner.align()
assert alignment == [1, 3, 4, 5, 7, 9, 10]