def test_offset(complicated_offset):
pileup = SparseValues(
# 1 1 2--3 4 5---6 7 8
np.array([0, 1, 2, 4, 6, 8, 10, 12, 14], dtype="int"),
np.array([1, 0, 1, 0, 1, 0, 1, 0, 1], dtype="bool"))
holes = HolesCleaner(complicated_offset, pileup, 3).run()
true = SparseValues([0, 8, 10], [1, 0, 1])
assert holes == true
def test_internals():
graph = obg.GraphWithReversals({101: obg.Block(100)}, {101: []})
pileup = SparseValues([0, 10, 19, 30, 41, 50], [1, 0, 1, 0, 1, 0])
cleaned = HolesCleaner(graph, pileup, 10).run()
true = SparseValues([0, 30, 41, 50], [1, 0, 1, 0])
assert cleaned == true
def test_single_peak():
indices = np.array([0, 3, 32], dtype="int")
values = np.array([False, True, False], dtype="bool")
pileup = SparseValues(indices, values)
indices = np.arange(0, 40, 2)
values = (np.arange(0, 40, 2) + 1) % 5
score_pileup = SparseValues(indices, values)
score_pileup.track_size = 100
graph.node_indexes = np.arange(0, 110, 10)
max_paths = SparseMaxPaths(pileup, graph, score_pileup)
print(max_paths.run())
def convert_old_sparse(old_sparse):
graph = old_sparse.graph
indices = [0]
values = [0]
for key in sorted(old_sparse.data.keys()):
vi = old_sparse.data[key]
node_idx = graph.node_indexes[key - graph.min_node]
indices.append(node_idx)
values.append(vi.start_value)
indices.extend(vi.indexes + node_idx)
values.extend(vi.values)
sv = SparseValues(indices, values, sanitize=True)
sv.track_size = graph.node_indexes[-1]
return sv
def test_long_hole():
pileup = SparseValues([0, 5, 95], [True, False, True])
graph = obg.GraphWithReversals({i: obg.Block(1)
for i in range(1, 101)},
{i: [i + 1]
for i in range(1, 100)})
holes = HolesCleaner(graph, pileup, 56).run()
assert holes == pileup
def test_sample_equals_control_one_node(self):
sample = from_intervals(self.graph, [Interval(0, 3, [2])])
control = from_intervals(self.graph, [Interval(0, 3, [1, 2])])
finder = PValuesFinder(sample, control)
p_values = finder.get_p_values_pileup()
correct = SparseValues([0, 3, 6], [0, -np.log10(0.26424), 0])
self.assertEqual(p_values, correct)
def test_holes_cleaner():
indices = np.array(
[80, 100, 180, 220, 240, 250, 300, 400, 500, 520, 610, 810])
values = np.array([(i % 2) for i, _ in enumerate(indices)])
pileup = SparseValues(indices, values)
graph = obg.GraphWithReversals({i + 1: obg.Block(100)
for i in range(10)},
{i: [i + 1]
for i in range(1, 10)})
# graph.node_indexes = np.arange(0, 1001, 100)
holes = HolesCleaner(graph, pileup, 10).run()
print(holes)
def test_simple_peak():
pileup = SparseValues([0, 5, 35], [False, True, False])
score_pileup = SparseValues([0, 5, 10, 20, 30, 35], [0, 1, 2, 3, 4, 0])
score_pileup.track_size = 100
pileup.track_size = 100
max_paths = SparseMaxPaths(pileup, graph, score_pileup).run()
assert max_paths == [Peak(5, 5, [1, 3, 4], graph=graph)]
def test_get_summits(self):
qvalues = SparseValues(np.array([0]), np.array([3]))
qvalues.track_size = 22
qvalues.to_sparse_files("tests/test_qvalues")
run_argument_parser([
"create_ob_graph", "-o", "tests/testgraph.obg",
"tests/vg_test_graph.json"
])
max_paths = PeakCollection([Peak(0, 2, [1, 2], score=3)])
PeakFasta(self.correct_sequence_graph).write_max_path_sequences(
"tests/test_max_paths.fasta", max_paths)
run_argument_parser([
"get_summits", "-g", "tests/testgraph.obg",
"tests/test_max_paths.fasta", "tests/test_qvalues", "2"
])
result = PeakCollection.from_fasta_file(
"tests/test_max_paths_summits.fasta")
self.assertEqual(result.intervals[0], Peak(2, 6, [1]))
self.assertEqual(result.intervals[0].sequence.lower(), "tccc")
def test_offset_end_peak():
graph = offsetgraph()
pileup = SparseValues([0, 85], [False, True])
score_pileup = SparseValues([0, 85], [0, 10])
score_pileup.track_size = 100
pileup.track_size = 100
max_paths = SparseMaxPaths(pileup, graph, score_pileup).run()
print(max_paths)
assert max_paths == [Peak(5, 10, [109, 110], graph=graph)]
def test_trailing_zeros():
graph = offsetgraph()
pileup = SparseValues([0, 5, 35], [False, True, False])
score_pileup = SparseValues([0, 15, 30], [0, 10, 0])
score_pileup.track_size = 100
pileup.track_size = 100
max_paths = SparseMaxPaths(pileup, graph, score_pileup).run()
print(max_paths)
assert max_paths == [Peak(5, 5, [101, 103, 104], graph=graph)]
def test_to_from_file(self):
indexes = np.array([1, 2, 3, 4, 5, 6, 7, 8])
values = np.array([1, 2, 3, 4, 5, 6, 7, 8])
sv = SparseValues(indexes, values)
sv.track_size = 10
sv.to_sparse_files("test_sparsevalues.tmp")
new = sv.from_sparse_files("test_sparsevalues.tmp")
self.assertEqual(sv, new)
def test_multiple_peak():
graph = complicated_offset()
pileup = SparseValues([0, 1, 7, 8, 10, 12, 14], [0, 1, 0, 1, 0, 1, 0])
score_pileup = SparseValues([0, 4], [5, 6])
score_pileup.track_size = 20
pileup.track_size = 20
max_paths = SparseMaxPaths(pileup, graph, score_pileup).run()
max_paths.sort(key=lambda x: x.region_paths[0])
print(max_paths)
assert max_paths == [
Peak(1, 1, [101, 103, 104], graph=graph),
Peak(0, 2, [105, 107], graph=graph)
]
import logging
logging.basicConfig(level=logging.DEBUG)
from offsetbasedgraph import Graph, NumpyIndexedInterval
from offsetbasedgraph.vcfmap import load_variant_maps
from graph_peak_caller.postprocess.maxpaths import SparseMaxPaths
from graph_peak_caller.sparsediffs import SparseValues
from graph_peak_caller.peakcollection import PeakCollection
chrom = sys.argv[1]
fragment_length = int(sys.argv[2])
ref = NumpyIndexedInterval.from_file("/data/bioinf/tair2/" + chrom + "_linear_pathv2.interval")
graph = Graph.from_file("/data/bioinf/tair2/" + chrom + ".nobg")
direct = SparseValues.from_sparse_files(chrom + "_direct_pileup")
filtered_peaks = SparseValues.from_sparse_files(chrom + "_hole_cleaned")
variant_map = load_variant_maps(chrom, "/data/bioinf/tair2/")
max_paths, sub_graphs = SparseMaxPaths(filtered_peaks, graph, direct, ref, variant_map).run()
long_maxpaths = [path for path in max_paths if path.length() >= fragment_length]
for max_path in long_max_paths:
assert max_path.length() > 0, "Max path %s has negative length" % max_path
score = np.max(self.q_values.get_interval_values(max_path))
max_path.set_score(score)
assert not np.isnan(score), "Score %s is nan" % score
PeakCollection(long_maxpaths).to_file(chrom + "_max_paths.intervalcollection", text_file=True)
def nonvar_pileup():
sv = SparseValues([0, 15, 45, 50, 60, 70], [0, 1, 4, 1, 3, 5])
sv.track_size = 80
return sv
def pileup():
sv = SparseValues([0, 15, 30, 45, 50, 60, 70], [0, 1, 2, 6, 2, 3, 6])
sv.track_size = 80
return sv
def test_end_hole():
pileup = SparseValues([0, 5, 10], [False, True, False])
graph = obg.GraphWithReversals({1: obg.Block(12)}, {1: []})
holes = HolesCleaner(graph, pileup, 4).run()
assert holes == pileup
def areas():
sv = SparseValues([0, 15, 42, 48, 72], [0, 1, 0, 1, 0])
sv.track_size = 80
return sv
def test_non_touched_mid(small_graph):
touched_nodes = set([101, 102, 103, 104, 105, 106])
pileup = SparseValues([0, 4, 22, 28, 56], [1, 0, 1, 0, 1])
cleaned = HolesCleaner(small_graph, pileup, 20, touched_nodes).run()
true = SparseValues([0, 30, 40], [1, 0, 1])
assert cleaned == true
def test_touched_edge(small_graph):
touched_nodes = set([101, 103, 106])
pileup = SparseValues([0, 4, 22, 28, 56], [1, 0, 1, 0, 1])
cleaned = HolesCleaner(small_graph, pileup, 4, touched_nodes).run()
assert cleaned == pileup
def offset_areas():
sv = SparseValues([0, 10, 11, 20, 29, 31], [1, 0, 1, 0, 1, 0])
sv.track_size = 80
return sv