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")