def set_graph(self):
self.fragment_length = 5
self.read_length = 1
self.graph = GraphWithReversals({i: Block(15)
for i in range(1, 5)}, {
1: [2, 3],
2: [4],
3: [4]
})
LinearMap.from_graph(self.graph).to_file("test_linear_map.npz")
def set_graph(self):
self.fragment_length = 6
self.read_length = 2
blocks = {i: Block(3) for i in range(1, 11)}
blocks[11] = Block(1000)
self.graph = GraphWithReversals(
blocks, {
1: [2, 3],
2: [7, 8],
3: [4, 5],
4: [6],
5: [6],
6: [10],
7: [9],
8: [9],
9: [10],
10: [11]
})
LinearMap.from_graph(self.graph).to_file("test_linear_map.npz")
def _create_data(self):
node_offset = 1
for chrom_number, chromosome in enumerate(self.chromosomes):
graph = Graph(
{i + node_offset: Block(10)
for i in range(0, 3)},
{i + node_offset: [i + 1 + node_offset]
for i in range(0, 2)})
linear_map = LinearMap.from_graph(graph)
linear_map_file_name = "linear_map_%s.npz" % chromosome
linear_map.to_file(linear_map_file_name)
self.linear_maps.append(linear_map_file_name)
self.sequence_retrievers.append(
SequenceRetriever(
{i + node_offset: "A" * 10
for i in range(0, 3)}))
self._create_reads(chrom_number, chromosome, graph)
node_offset += 3
graph.convert_to_numpy_backend()
SequenceGraph.create_empty_from_ob_graph(graph).to_file(
chromosome + ".nobg.sequences")
graph.to_file(chromosome + ".nobg")
def test_from_snp_graph(snp_graph, snp_map):
linear_map = LinearMap.from_graph(snp_graph)
assert linear_map == snp_map
def test_from_graph(hierarchical_graph, hierarchical_map):
linear_map = LinearMap.from_graph(hierarchical_graph)
assert linear_map == hierarchical_map
def snp_map():
true_starts = [0, 1, 1, 2, 2, 4]
true_ends = [1, 4, 2, 4, 4, 6]
return LinearMap(true_starts, true_ends, hierarchical_graph())
def hierarchical_map():
true_starts = [0, 10, 10, 22, 22, 36]
true_ends = [10, 36, 22, 36, 36, 51]
return LinearMap(true_starts, true_ends, hierarchical_graph())