Illegal slicing argument for scalar dataspace when attempting to read 10x_h5 with version 1.9.0 #2203
Comments
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Can you share the output of I'm unable to reproduce with recent cellranger outputs. |
ivirshup
added
Bug 🐛
Needs info❔
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Hey sorry for the delay: |
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I got similar error when I was trying to use .h5 file from cellbender output. I have multiome data. `>>> adata = scanpy.read_10x_h5("/sc/arion/projects/hmDNAmap/snHeroin/analysis/ARC_TD005235-354/outs/cellbender/cb_feature_bc_matrix_filtered.h5", gex_only=False)`
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/scanpy/readwrite.py", line 183, in read_10x_h5
adata = _read_v3_10x_h5(filename, start=start)
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/scanpy/readwrite.py", line 268, in _read_v3_10x_h5
_collect_datasets(dsets, f["matrix"])
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/scanpy/readwrite.py", line 256, in _collect_datasets
dsets[k] = v[:]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/h5py/_hl/dataset.py", line 738, in __getitem__
selection = sel2.select_read(fspace, args)
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/h5py/_hl/selections2.py", line 101, in select_read
return ScalarReadSelection(fspace, args)
File "/sc/arion/work/gujarh01/software/anaconda3/lib/python3.9/site-packages/h5py/_hl/selections2.py", line 86, in __init__
raise ValueError("Illegal slicing argument for scalar dataspace")
> **ValueError: Illegal slicing argument for scalar dataspace**
anndata 0.8.0 PIL 8.4.0 Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] Session information updated at 2022-05-17 14:56 |
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I'm getting the same error using the CellBender tutorial output. Attaching the file to make it easier to reproduce.
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Was this fixed by #2344 ? Edit: Yes |
* Handle scalar datasets too After @ivirshup's pytables PR (#2064) we started having issues with loading h5 files with scalar datasets, such as those created by CellBender (broadinstitute/CellBender#128). It is currently not an issue for the 10X h5 files for now since they don't have any scalars, however it'd be good to just handle scalars as well as arrays 1- to fix the cellbender file loading problem 2- to fix potential problems we might end up having if 10X h5 format includes scalar datasets. * Add a scalar to the multiple_genomes.h5 test file * Fixes #2203
Hi
When attempting so simply read a h5 file with:
I get the following error which is fixed when rolling back to scanpy=1.8.2
ValueError Traceback (most recent call last) <ipython-input-3-8ddd0a13aab2> in <module> 8 print(results_file) ----> 9 adata = sc.read_10x_h5(results_file) 10 adata.var_names_make_unique() 11 adata.obs.index = meta.iloc[idx,2] + '-' + adata.obs.index /opt/conda/lib/python3.8/site-packages/scanpy/readwrite.py in read_10x_h5(filename, genome, gex_only, backup_url) 181 v3 = '/matrix' in f 182 if v3: --> 183 adata = _read_v3_10x_h5(filename, start=start) 184 if genome: 185 if genome not in adata.var['genome'].values: /opt/conda/lib/python3.8/site-packages/scanpy/readwrite.py in _read_v3_10x_h5(filename, start) 266 try: 267 dsets = {} --> 268 _collect_datasets(dsets, f["matrix"]) 269 270 from scipy.sparse import csr_matrix /opt/conda/lib/python3.8/site-packages/scanpy/readwrite.py in _collect_datasets(dsets, group) 254 for k, v in group.items(): 255 if isinstance(v, h5py.Dataset): --> 256 dsets[k] = v[:] 257 else: 258 _collect_datasets(dsets, v) h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() /opt/conda/lib/python3.8/site-packages/h5py/_hl/dataset.py in __getitem__(self, args, new_dtype) 767 if self.shape == (): 768 fspace = self.id.get_space() --> 769 selection = sel2.select_read(fspace, args) 770 if selection.mshape is None: 771 arr = numpy.ndarray((), dtype=new_dtype) /opt/conda/lib/python3.8/site-packages/h5py/_hl/selections2.py in select_read(fspace, args) 99 """ 100 if fspace.shape == (): --> 101 return ScalarReadSelection(fspace, args) 102 103 raise NotImplementedError() /opt/conda/lib/python3.8/site-packages/h5py/_hl/selections2.py in __init__(self, fspace, args) 84 self.mshape = () 85 else: ---> 86 raise ValueError("Illegal slicing argument for scalar dataspace") 87 88 self.mspace = h5s.create(h5s.SCALAR) ValueError: Illegal slicing argument for scalar dataspaceThanks!!
Nadav
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