SingleCellExperiment 0.5.6__tar.gz → 0.5.7__tar.gz

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/.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: v0.9.3
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/AUTHORS.md

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

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## 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.

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: SingleCellExperiment
-Version: 0.5.6
+Version: 0.5.7
 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-0.5.7}/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-0.5.7}/docs/authors.md

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

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/docs/changelog.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## 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.

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/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-0.5.7}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: SingleCellExperiment
-Version: 0.5.6
+Version: 0.5.7
 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-0.5.7}/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-0.5.7}/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)

{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/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-0.5.7/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-0.5.7/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-0.5.7/tests/data/raw_feature_bc_matrix/matrix.mtx

@@ -0,0 +1,340 @@
+%%MatrixMarket matrix coordinate integer general
+50 50 338
+13 1 1
+16 1 1
+26 1 1
+29 1 1
+37 1 3
+38 1 1
+45 1 1
+7 2 1
+8 2 1
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{singlecellexperiment-0.5.6 → singlecellexperiment-0.5.7}/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")