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_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")