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Something wrong with read_10x_mtx using anndata-0.10.4 #2822

Closed
2 of 3 tasks
aStudyingTurtle opened this issue Jan 23, 2024 · 1 comment
Closed
2 of 3 tasks

Something wrong with read_10x_mtx using anndata-0.10.4 #2822

aStudyingTurtle opened this issue Jan 23, 2024 · 1 comment
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Bug 🐛

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@aStudyingTurtle
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Please make sure these conditions are met

  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • (optional) I have confirmed this bug exists on the master branch of scanpy.

What happened?

When I install scanpy==1.9.6 with pip (anndata==0.10.4), something wrong and adata.X.nnz is 0.
I changed the version of anndata to 0.9.2, it works normal.

Minimal code sample

import numpy as np
import pandas as pd
import scanpy as sc
sc.settings.verbosity = 3             # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.logging.print_header()
sc.settings.set_figure_params(dpi=80, facecolor='white')
results_file = 'write/pbmc3k.h5ad'  # the file that will store the analysis results
adata = sc.read_10x_mtx(my_sample,  # the directory with the `.mtx` file
    var_names='gene_symbols',                # use gene symbols for the variable names (variables-axis index)
    cache=False)                              # write a cache file for faster subsequent reading
# sc.pl.highest_expr_genes(adata, n_top=20, )
adata.X.nnz

Error output

No response

Versions


-----
anndata     0.9.2
scanpy      1.9.5
-----
PIL                 9.5.0
asttokens           NA
backcall            0.2.0
bottleneck          1.3.5
cffi                1.16.0
comm                0.1.2
cycler              0.12.0
cython_runtime      NA
dateutil            2.8.2
debugpy             1.6.7
decorator           4.4.2
defusedxml          0.7.1
entrypoints         0.4
executing           1.2.0
google              NA
h5py                3.7.0
hurry               NA
ipykernel           6.25.0
ipython_genutils    0.2.0
ipywidgets          8.0.4
jedi                0.18.1
joblib              1.2.0
kiwisolver          1.4.5
llvmlite            0.41.1
matplotlib          3.8.0
matplotlib_inline   0.1.6
mpl_toolkits        NA
natsort             8.4.0
numba               0.58.1
numexpr             2.8.7
numpy               1.26.0
packaging           23.2
pandas              1.5.3
parso               0.8.3
patsy               0.5.6
pexpect             4.8.0
pickleshare         0.7.5
pkg_resources       NA
platformdirs        3.10.0
prompt_toolkit      3.0.36
psutil              5.9.0
ptyprocess          0.7.0
pure_eval           0.2.2
pyarrow             13.0.0
pycparser           2.21
pydev_ipython       NA
pydevconsole        NA
pydevd              2.9.5
pydevd_file_utils   NA
pydevd_plugins      NA
pydevd_tracing      NA
pygments            2.15.1
pynndescent         0.5.11
pyparsing           3.0.9
pytz                2023.3.post1
ruamel              NA
scipy               1.11.3
session_info        1.0.0
setuptools          68.0.0
setuptools_scm      NA
six                 1.16.0
sklearn             1.3.0
sphinxcontrib       NA
stack_data          0.2.0
statsmodels         0.14.1
threadpoolctl       3.1.0
tornado             6.3.3
tqdm                4.65.0
traitlets           5.7.1
typing_extensions   NA
umap                0.5.5
wcwidth             0.2.5
yaml                6.0.1
zmq                 23.2.0
zoneinfo            NA
zstandard           0.19.0
-----
IPython             8.12.0
jupyter_client      7.4.9
jupyter_core        5.5.0
notebook            6.5.4
-----
Python 3.10.11 (main, May 16 2023, 00:28:57) [GCC 11.2.0]
Linux-6.2.0-37-generic-x86_64-with-glibc2.35
-----
Session information updated at 2024-01-23 21:45
@flying-sheep flying-sheep changed the title Something wrong when read 10X_mtx with anndata-0.10.4 Something wrong with read_10x_mtx using anndata-0.10.4 Jan 23, 2024
@flying-sheep
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flying-sheep commented Jan 23, 2024 •
edited
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Please check recently closed bugs before filing a new one: #2806 (comment)

If you think this is still an issue with the newest scanpy version, please say so and we can reopen this

@flying-sheep flying-sheep closed this as not planned Won't fix, can't repro, duplicate, stale Jan 23, 2024
@flying-sheep flying-sheep mentioned this issue Jan 25, 2024
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