SingleCellExperiment 0.5.6__tar.gz → 0.5.8__tar.gz

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.6
+  rev: v0.9.10
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/AUTHORS.md

@@ -1,3 +1,4 @@
 # Contributors
 
 * jkanche <jayaram.kancherla@gmail.com>
+* keviny2 <kevinyang10@gmail.com>

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/CHANGELOG.md

@@ -1,12 +1,22 @@
 # Changelog
 
+## Version 0.5.8
+
+- Rename `reduced_dims` to `reduced_dimensions`. Constructor accepts both these arguments for backwards compatibility.
+- Additionally, SCE's constructor takes kwargs for future proofing any additional attributes in the upstream classes.
+
+## Version 0.5.7
+
+- Support reading outputs from CellRanger version 3 and later in `read_tenx_mtx`.
+  - Handle both `genes.csv` and `features.csv` for gene annotations.
+
 ## Version 0.5.6
 
-- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the ``withDimnames`` parameter in the R implementation.
+- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the `withDimnames` parameter in the R implementation.
   - On **getters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **replaced** with the
-  column names of the main experiment.
+    column names of the main experiment.
   - On **setters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **checked** with the
-  column names of the main experiment and an Exception is raised if they do not match.
+    column names of the main experiment and an Exception is raised if they do not match.
 
 ## Version 0.5.1 - 0.5.5
 
@@ -15,7 +25,6 @@
 - Add getters and setters to replace a specific alternative experiment or reduced dimension.
 - Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils's subset functions to perform these operations.
 
-
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: SingleCellExperiment
-Version: 0.5.6
+Version: 0.5.8
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -58,7 +58,7 @@ pip install singlecellexperiment
 
 ## Usage
 
-The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+The `SingleCellExperiment` extends [RangedSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
 
 - `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
 - `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
@@ -98,7 +98,7 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Since `SingleCellExperiment` extends `RangedSummarizedExperiment`, most methods especially slicing and accessors are inherited from the parent classes.
 Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/README.md

@@ -17,7 +17,7 @@ pip install singlecellexperiment
 
 ## Usage
 
-The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+The `SingleCellExperiment` extends [RangedSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
 
 - `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
 - `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
@@ -57,7 +57,7 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Since `SingleCellExperiment` extends `RangedSummarizedExperiment`, most methods especially slicing and accessors are inherited from the parent classes.
 Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/docs/authors.md

@@ -1,3 +1,4 @@
 # Contributors
 
 * jkanche <jayaram.kancherla@gmail.com>
+* keviny2 <kevinyang10@gmail.com>

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/docs/changelog.md

@@ -1,12 +1,22 @@
 # Changelog
 
+## Version 0.5.8
+
+- Rename `reduced_dims` to `reduced_dimensions`. Constructor accepts both these arguments for backwards compatibility.
+- Additionally, SCE's constructor takes kwargs for future proofing any additional attributes in the upstream classes.
+
+## Version 0.5.7
+
+- Support reading outputs from CellRanger version 3 and later in `read_tenx_mtx`.
+  - Handle both `genes.csv` and `features.csv` for gene annotations.
+
 ## Version 0.5.6
 
-- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the ``withDimnames`` parameter in the R implementation.
+- Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the `withDimnames` parameter in the R implementation.
   - On **getters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **replaced** with the
-  column names of the main experiment.
+    column names of the main experiment.
   - On **setters** of alternative experiments, if `with_dim_names` is True, column names of the alternative experiment are **checked** with the
-  column names of the main experiment and an Exception is raised if they do not match.
+    column names of the main experiment and an Exception is raised if they do not match.
 
 ## Version 0.5.1 - 0.5.5
 
@@ -15,7 +25,6 @@
 - Add getters and setters to replace a specific alternative experiment or reduced dimension.
 - Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils's subset functions to perform these operations.
 
-
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/docs/readme.md

@@ -17,7 +17,7 @@ pip install singlecellexperiment
 
 ## Usage
 
-The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+The `SingleCellExperiment` extends [RangedSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
 
 - `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
 - `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
@@ -57,7 +57,7 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Since `SingleCellExperiment` extends `RangedSummarizedExperiment`, most methods especially slicing and accessors are inherited from the parent classes.
 Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: SingleCellExperiment
-Version: 0.5.6
+Version: 0.5.8
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -58,7 +58,7 @@ pip install singlecellexperiment
 
 ## Usage
 
-The `SingleCellExperiment` extends [RangeSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
+The `SingleCellExperiment` extends [RangedSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:
 
 - `reduced_dims`: Slot for low-dimensionality embeddings for each cell.
 - `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.
@@ -98,7 +98,7 @@ tse = SingleCellExperiment(
 )
 ```
 
-Since `SingleCellExperiment` extends `RangeSummarizedExperiment`, most methods especially slicing and accessors are applicable here.
+Since `SingleCellExperiment` extends `RangedSummarizedExperiment`, most methods especially slicing and accessors are inherited from the parent classes.
 Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.
 
 <!-- pyscaffold-notes -->

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/src/SingleCellExperiment.egg-info/SOURCES.txt

@@ -46,4 +46,7 @@ tests/test_sce_methods.py
 tests/test_sce_slice.py
 tests/data/adata.h5ad
 tests/data/mocks.py
-tests/data/tenx.sub.h5
+tests/data/tenx.sub.h5
+tests/data/raw_feature_bc_matrix/barcodes.tsv
+tests/data/raw_feature_bc_matrix/features.tsv
+tests/data/raw_feature_bc_matrix/matrix.mtx

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/src/singlecellexperiment/SingleCellExperiment.py

@@ -38,7 +38,7 @@ def _validate_reduced_dims(reduced_dims, shape):
     for rdname, mat in reduced_dims.items():
         if not hasattr(mat, "shape"):
             raise TypeError(
-                f"Reduced dimension: '{rdname}' must be a matrix-like object." "Does not contain a `shape` property."
+                f"Reduced dimension: '{rdname}' must be a matrix-like object.Does not contain a `shape` property."
             )
 
         if shape[1] != mat.shape[0]:
@@ -60,7 +60,7 @@ def _validate_alternative_experiments(alternative_experiments, shape, column_nam
             )
 
         if shape[1] != alternative_experiment.shape[1]:
-            raise ValueError(f"Alternative experiment: '{alt_name}' does not contain same number of" " cells.")
+            raise ValueError(f"Alternative experiment: '{alt_name}' does not contain same number of cells.")
 
         _alt_cnames = alternative_experiment.get_column_names()
         _alt_cnames = None if _alt_cnames is None else list(_alt_cnames)
@@ -94,7 +94,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
     parent experiment. Otherwise, these cells do not share the same sample or annotations
     and cannot be set in alternative experiments!
 
-    Note: Validation checks do not apply to ``row_pairs`` or ``col_pairs``.
+    Note: Validation checks do not apply to ``row_pairs`` or ``column_pairs``.
     """
 
     def __init__(
@@ -106,13 +106,15 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
         metadata: Optional[dict] = None,
-        reduced_dims: Optional[Dict[str, Any]] = None,
+        reduced_dimensions: Optional[Dict[str, Any]] = None,
+        reduced_dims: Optional[Dict[str, Any]] = None,  # deprecated name
         main_experiment_name: Optional[str] = None,
         alternative_experiments: Optional[Dict[str, Any]] = None,
         row_pairs: Optional[Any] = None,
         column_pairs: Optional[Any] = None,
         alternative_experiment_check_dim_names: bool = True,
         validate: bool = True,
+        **kwargs,
     ) -> None:
         """Initialize a single-cell experiment.
 
@@ -157,7 +159,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
                 Additional experimental metadata describing the methods.
                 Defaults to None.
 
-            reduced_dims:
+            reduced_dimensions:
                 Slot for low-dimensionality embeddings.
 
                 Usually a dictionary with the embedding method as keys (e.g., t-SNE, UMAP)
@@ -165,6 +167,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
                 Embeddings may be represented as a matrix or a data frame, must contain a shape.
 
+            reduced_dims:
+                Will be deprecated in the future versions. Use py:attr:`~reduced_dimensions` instead.
+
             main_experiment_name:
                 A string, specifying the main experiment name.
 
@@ -195,6 +200,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
             validate:
                 Internal use only.
+
+            kwargs:
+                Additional arguments.
         """
 
         super().__init__(
@@ -206,10 +214,20 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             column_names=column_names,
             metadata=metadata,
             validate=validate,
+            **kwargs,
         )
         self._main_experiment_name = main_experiment_name
 
-        self._reduced_dims = reduced_dims if reduced_dims is not None else {}
+        _dims = None
+        if reduced_dimensions is not None and reduced_dims is not None:
+            raise ValueError("Either 'reduced_dims' or 'reduced_dimensions' should be provided, but not both.")
+        elif reduced_dims is not None:
+            warn("'reduced_dims' is deprecated, use 'reduced_dimensions' instead.", DeprecationWarning)
+            _dims = reduced_dims
+        elif reduced_dimensions is not None:
+            _dims = reduced_dimensions
+
+        self._reduced_dims = _dims if _dims is not None else {}
 
         self._alternative_experiments = alternative_experiments if alternative_experiments is not None else {}
 
@@ -551,6 +569,10 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """Alias for :py:meth:`~get_reduced_dimension`, for back-compatibility."""
         return self.get_reduced_dimension(name=name)
 
+    def reduced_dimension(self, name: Union[str, int]) -> Any:
+        """Alias for :py:meth:`~get_reduced_dimension`, for back-compatibility."""
+        return self.get_reduced_dimension(name=name)
+
     def set_reduced_dimension(self, name: str, embedding: Any, in_place: bool = False) -> "SingleCellExperiment":
         """Add or replace :py:attr:`~singlecellexperiment.SingleCellExperiment.reduced_dimension`'s.
 

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/src/singlecellexperiment/io/tenx.py

@@ -1,11 +1,12 @@
+import os
 from warnings import warn
 
 from biocframe import BiocFrame, from_pandas
 
 from ..SingleCellExperiment import SingleCellExperiment
 
-__author__ = "jkanche"
-__copyright__ = "jkanche"
+__author__ = "jkanche, keviny2"
+__copyright__ = "jkanche, keviny2"
 __license__ = "MIT"
 
 
@@ -17,8 +18,9 @@ def read_tenx_mtx(path: str) -> SingleCellExperiment:
             Path to 10X MTX directory.
 
             Directory must contain `matrix.mtx`, and optionally
-            a `genes.tsv` to represent featires and `barcodes.tsv` for cell
-            annotations.
+            `genes.tsv` (CellRanger version 2) or
+            `features.tsv` (CellRanger version 3 and later) to
+            represent features and `barcodes.tsv` for cell annotations.
 
     Returns:
         A single-cell experiment object.
@@ -31,7 +33,18 @@ def read_tenx_mtx(path: str) -> SingleCellExperiment:
     mat = mmread(f"{path}/matrix.mtx")
     mat = csr_matrix(mat)
 
-    genes = pd.read_csv(path + "/genes.tsv", header=None, sep="\t")
+    features_path = path + "/features.tsv"
+    genes_path = path + "/genes.tsv"
+    if os.path.exists(features_path) and os.path.exists(genes_path):
+        warn(
+            "Both 'features.tsv' and 'genes.tsv' files are present in the directory. "
+            "Prioritizing 'features.tsv' for processing."
+        )
+
+    if os.path.exists(features_path):
+        genes = pd.read_csv(features_path, header=None, sep="\t", usecols=[0, 1])
+    else:
+        genes = pd.read_csv(genes_path, header=None, sep="\t")
     genes.columns = ["gene_ids", "gene_symbols"]
 
     cells = pd.read_csv(path + "/barcodes.tsv", header=None, sep="\t")

singlecellexperiment-0.5.8/tests/data/raw_feature_bc_matrix/barcodes.tsv

@@ -0,0 +1,50 @@
+AAACAACGAATAGTTC-1
+AAACAAGTATCTCCCA-1
+AAACAATCTACTAGCA-1
+AAACACCAATAACTGC-1
+AAACAGAGCGACTCCT-1
+AAACAGCTTTCAGAAG-1
+AAACAGGGTCTATATT-1
+AAACAGTGTTCCTGGG-1
+AAACATGGTGAGAGGA-1
+AAACATTTCCCGGATT-1
+AAACCACTACACAGAT-1
+AAACCCGAACGAAATC-1
+AAACCGGAAATGTTAA-1
+AAACCGGGTAGGTACC-1
+AAACCGTTCGTCCAGG-1
+AAACCTAAGCAGCCGG-1
+AAACCTCATGAAGTTG-1
+AAACGAAGAACATACC-1
+AAACGAAGATGGAGTA-1
+AAACGACAGTCTTGCC-1
+AAACGAGACGGTTGAT-1
+AAACGCCCGAGATCGG-1
+AAACGCTGGGCACGAC-1
+AAACGGGCGTACGGGT-1
+AAACGGGTTGGTATCC-1
+AAACGGTTGCGAACTG-1
+AAACGTGTTCGCCCTA-1
+AAACTAACGTGGCGAC-1
+AAACTCGGTTCGCAAT-1
+AAACTCGTGATATAAG-1
+AAACTGCTGGCTCCAA-1
+AAACTTAATTGCACGC-1
+AAACTTGCAAACGTAT-1
+AAAGAATGACCTTAGA-1
+AAAGAATGTGGACTAA-1
+AAAGACATGAAGTTTA-1
+AAAGACCCAAGTCGCG-1
+AAAGACTGGGCGCTTT-1
+AAAGCTTGCCTACATA-1
+AAAGGCCCTATAATAC-1
+AAAGGCTACGGACCAT-1
+AAAGGCTCTCGCGCCG-1
+AAAGGGATGTAGCAAG-1
+AAAGGGCAGCTTGAAT-1
+AAAGGTAAGCTGTACC-1
+AAAGGTCAACGACATG-1
+AAAGTAGCATTGCTCA-1
+AAAGTCACTGATGTAA-1
+AAAGTCGACCCTCAGT-1
+AAAGTGCCATCAATTA-1

singlecellexperiment-0.5.8/tests/data/raw_feature_bc_matrix/features.tsv

@@ -0,0 +1,50 @@
+ENSMUSG00000051951	Xkr4	Gene Expression
+ENSMUSG00000089699	Gm1992	Gene Expression
+ENSMUSG00000102343	Gm37381	Gene Expression
+ENSMUSG00000025900	Rp1	Gene Expression
+ENSMUSG00000025902	Sox17	Gene Expression
+ENSMUSG00000104328	Gm37323	Gene Expression
+ENSMUSG00000033845	Mrpl15	Gene Expression
+ENSMUSG00000025903	Lypla1	Gene Expression
+ENSMUSG00000104217	Gm37988	Gene Expression
+ENSMUSG00000033813	Tcea1	Gene Expression
+ENSMUSG00000002459	Rgs20	Gene Expression
+ENSMUSG00000085623	Gm16041	Gene Expression
+ENSMUSG00000033793	Atp6v1h	Gene Expression
+ENSMUSG00000025905	Oprk1	Gene Expression
+ENSMUSG00000033774	Npbwr1	Gene Expression
+ENSMUSG00000025907	Rb1cc1	Gene Expression
+ENSMUSG00000090031	4732440D04Rik	Gene Expression
+ENSMUSG00000087247	Alkal1	Gene Expression
+ENSMUSG00000033740	St18	Gene Expression
+ENSMUSG00000051285	Pcmtd1	Gene Expression
+ENSMUSG00000097797	Gm26901	Gene Expression
+ENSMUSG00000103067	Gm30414	Gene Expression
+ENSMUSG00000025909	Sntg1	Gene Expression
+ENSMUSG00000061024	Rrs1	Gene Expression
+ENSMUSG00000025911	Adhfe1	Gene Expression
+ENSMUSG00000067879	3110035E14Rik	Gene Expression
+ENSMUSG00000099827	Gm29520	Gene Expression
+ENSMUSG00000025912	Mybl1	Gene Expression
+ENSMUSG00000045210	Vcpip1	Gene Expression
+ENSMUSG00000097893	1700034P13Rik	Gene Expression
+ENSMUSG00000025915	Sgk3	Gene Expression
+ENSMUSG00000046101	Mcmdc2	Gene Expression
+ENSMUSG00000098234	Snhg6	Gene Expression
+ENSMUSG00000099032	Tcf24	Gene Expression
+ENSMUSG00000025916	Ppp1r42	Gene Expression
+ENSMUSG00000087199	Gm15818	Gene Expression
+ENSMUSG00000025917	Cops5	Gene Expression
+ENSMUSG00000056763	Cspp1	Gene Expression
+ENSMUSG00000067851	Arfgef1	Gene Expression
+ENSMUSG00000042501	Cpa6	Gene Expression
+ENSMUSG00000048960	Prex2	Gene Expression
+ENSMUSG00000057715	A830018L16Rik	Gene Expression
+ENSMUSG00000097171	Gm17644	Gene Expression
+ENSMUSG00000101314	Gm29663	Gene Expression
+ENSMUSG00000016918	Sulf1	Gene Expression
+ENSMUSG00000025938	Slco5a1	Gene Expression
+ENSMUSG00000099498	Gm29283	Gene Expression
+ENSMUSG00000042414	Prdm14	Gene Expression
+ENSMUSG00000005886	Ncoa2	Gene Expression
+ENSMUSG00000101476	Gm29570	Gene Expression

singlecellexperiment-0.5.8/tests/data/raw_feature_bc_matrix/matrix.mtx

@@ -0,0 +1,340 @@
+%%MatrixMarket matrix coordinate integer general
+50 50 338
+13 1 1
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{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/tests/test_sce.py

@@ -172,3 +172,48 @@ def test_SCE_different_alt_names():
             column_data=pd.DataFrame(index = ["ChIP", "Input", "Input"] * 2),
             alternative_experiments={"alt": rse},
         )
+
+def test_SCE_dims():
+    embeds = np.random.rand(counts.shape[1], 4)
+    tse = SingleCellExperiment(
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dimensions={
+            "something": embeds
+        }
+    )
+
+    assert tse is not None
+    assert isinstance(tse, sce)
+    assert tse.get_reduced_dimension_names() == ["something"]
+
+    tse2 = SingleCellExperiment(
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dims={
+            "something": embeds
+        }
+    )
+
+    assert tse2 is not None
+    assert isinstance(tse2, sce)
+    assert tse2.get_reduced_dimension_names() == ["something"]
+
+    print(tse.get_reduced_dimension("something"), tse2.get_reduced_dimension("something"))
+
+    assert np.allclose(tse.get_reduced_dimension("something"), tse2.get_reduced_dimension("something"))
+
+    with pytest.raises(Exception, match="Either 'reduced_dims' or 'reduced_dimensions' should be provided, but not both."):
+        SingleCellExperiment(
+            assays={"counts": counts},
+            row_data=row_data,
+            column_data=col_data,
+            reduced_dims={
+                "something": embeds
+            },
+            reduced_dimensions={
+                "something": embeds
+            }
+        )

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.8}/tests/test_sce_io.py

@@ -12,8 +12,8 @@ import singlecellexperiment
 from singlecellexperiment.SingleCellExperiment import SingleCellExperiment
 from hdf5array import Hdf5CompressedSparseMatrix
 
-__author__ = "jkanche"
-__copyright__ = "jkanche"
+__author__ = "jkanche, keviny2"
+__copyright__ = "jkanche, keviny2"
 __license__ = "MIT"
 
 
@@ -90,6 +90,29 @@ def test_SCE_fromH5AD():
     assert sliced.shape == (10, 4)
 
 
+def test_SCE_from10x_mtx():
+    tse = singlecellexperiment.read_tenx_mtx("tests/data/raw_feature_bc_matrix")
+
+    assert tse is not None
+    assert isinstance(tse, SingleCellExperiment)
+
+    assert tse.assays is not None
+    assert tse.row_data is not None
+    assert tse.col_data is not None
+
+    # slice
+    sliced = tse[0:10, 1:5]
+
+    assert sliced is not None
+    assert isinstance(sliced, SingleCellExperiment)
+
+    assert sliced.assays is not None
+    assert sliced.row_data is not None
+    assert sliced.col_data is not None
+
+    assert sliced.shape == (10, 4)
+
+
 def test_SCE_from10xH5():
     tse = singlecellexperiment.read_tenx_h5("tests/data/tenx.sub.h5")