SingleCellExperiment 0.4.5__tar.gz → 0.4.6__tar.gz

{singlecellexperiment-0.4.5 → singlecellexperiment-0.4.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.5
+Version: 0.4.6
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{singlecellexperiment-0.4.5 → singlecellexperiment-0.4.6}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.5
+Version: 0.4.6
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{singlecellexperiment-0.4.5 → singlecellexperiment-0.4.6}/src/singlecellexperiment/io/tenx.py

@@ -44,7 +44,7 @@ def read_tenx_mtx(path: str) -> SingleCellExperiment:
     )
 
 
-def read_tenx_h5(path: str) -> SingleCellExperiment:
+def read_tenx_h5(path: str, realize_assays: bool = False) -> SingleCellExperiment:
     """Read 10X H5 file as :py:class:`~singlecellexperiment.SingleCellExperiment.SingleCellExperiment`.
 
     Note: Currently only supports version 3 of the 10X H5 format.
@@ -53,10 +53,15 @@ def read_tenx_h5(path: str) -> SingleCellExperiment:
         path:
             Path to 10x H5 file.
 
+        realize_assays:
+            Whether to realize assays into memory.
+            Defaults to False.
+
     Returns:
         A single-cell experiment object.
     """
 
+    import delayedarray as da
     import h5py
     from hdf5array import Hdf5CompressedSparseMatrix
 
@@ -74,6 +79,9 @@ def read_tenx_h5(path: str) -> SingleCellExperiment:
         path=path, group_name="matrix", by_column=True, shape=shape
     )
 
+    if realize_assays is True:
+        counts = da.to_scipy_sparse_matrix(counts, "csr")
+
     # read features
     features = None
     ignore_list = []

{singlecellexperiment-0.4.5 → singlecellexperiment-0.4.6}/tests/test_sce_io.py

@@ -6,9 +6,11 @@ from biocframe import BiocFrame
 import numpy as np
 import pandas as pd
 from mudata import MuData
+from scipy import sparse
 
 import singlecellexperiment
 from singlecellexperiment.SingleCellExperiment import SingleCellExperiment
+from hdf5array import Hdf5CompressedSparseMatrix
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"
@@ -95,6 +97,7 @@ def test_SCE_from10xH5():
     assert isinstance(tse, SingleCellExperiment)
 
     assert tse.assays is not None
+    assert isinstance(tse.assay(0), Hdf5CompressedSparseMatrix)
     assert tse.row_data is not None
     assert tse.col_data is not None
 
@@ -110,6 +113,11 @@ def test_SCE_from10xH5():
 
     assert sliced.shape == (10, 4)
 
+    tse = singlecellexperiment.read_tenx_h5(
+        "tests/data/tenx.sub.h5", realize_assays=True
+    )
+    assert isinstance(tse.assay(0), sparse.spmatrix)
+
 
 def test_SCE_randomAnnData():
     np.random.seed(1)