How to use the zarr.LMDBStore function in zarr

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github tskit-dev / tsinfer / tests / View on Github external
def test_zero_sequence_length(self):
        # Mangle a sample data file to force a zero sequence length.
        ts = msprime.simulate(10, mutation_rate=2, random_seed=5)
        with tempfile.TemporaryDirectory(prefix="tsinf_format_test") as tempdir:
            filename = os.path.join(tempdir, "samples.tmp")
            with tsinfer.SampleData(path=filename) as sample_data:
                for var in ts.variants():
                    sample_data.add_site(, var.genotypes)
            store = zarr.LMDBStore(filename, subdir=False)
            data =, mode="w+")
            data.attrs["sequence_length"] = 0
            sample_data = tsinfer.load(filename)
            self.assertEqual(sample_data.sequence_length, 0)
            self.assertRaises(ValueError, tsinfer.generate_ancestors, sample_data)
github tskit-dev / tsinfer / tsinfer / View on Github external
def _open_lmbd_readonly(self):
        # We set the mapsize here because LMBD will map 1TB of virtual memory if
        # we don't, making it hard to figure out how much memory we're actually
        # using.
        map_size = None
            map_size = os.path.getsize(self.path)
        except OSError as e:
            raise exceptions.FileFormatError(str(e)) from e
            store = zarr.LMDBStore(
                self.path, map_size=map_size, readonly=True, subdir=False, lock=False
        except lmdb.InvalidError as e:
            raise exceptions.FileFormatError(
                "Unknown file format:{}".format(str(e))
            ) from e
        except lmdb.Error as e:
            raise exceptions.FileFormatError(str(e)) from e
        return store
github tskit-dev / tsinfer / tsinfer / View on Github external
def _new_lmdb_store(self, map_size=None):
        if os.path.exists(self.path):
        # The existence of a lock-file can confuse things, so delete it.
        if map_size is None:
            map_size = DEFAULT_MAX_FILE_SIZE
            map_size = int(map_size)
            if map_size <= 0:
                raise ValueError("max_file_size must be > 0")
        return zarr.LMDBStore(self.path, subdir=False, map_size=map_size)