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I was trying to concatenate two large scRNA data set using the concat_on_disk. I confirmed that I have both scRNA data as csr_matrix. But I got the following errors saying 'csc','csc' is not supported, which doesn't make sense. I read the h5ad file into the memory and it is csr. But the concat_on_disk would identify it as csc. Could you please provide some hint what might be wrong here?
Code:
# confirm that sc1 and sc2 is csr matrix
>>> from scipy.sparse import csr_matrix
>>> sc1=sc.read("sc1.processed.h5ad")
>>> sc2=sc.read("sc2.processed.h5ad")
>>> isinstance(sc1.X, csr_matrix)
True
>>> isinstance(sc2.X, csr_matrix)
True
ad.experimental.concat_on_disk(dict(sc1="sc1.processed.h5ad",sc2="sc2.processed.h5ad"),out_file="test.h5ad",axis=0,label="source")
Traceback:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "~/myfolder/conda/envs/scvi-env/lib/python3.9/site-packages/anndata/experimental/merge.py", line 652, in concat_on_disk
_write_concat_mappings(
File "~/myfolder/conda/envs/scvi-env/lib/python3.9/site-packages/anndata/experimental/merge.py", line 262, in _write_concat_mappings
_write_concat_sequence(
File "~/myfolder/conda/envs/scvi-env/lib/python3.9/site-packages/anndata/experimental/merge.py", line 358, in _write_concat_sequence
_write_concat_arrays(
File "~/myfolder/conda/envs/scvi-env/lib/python3.9/site-packages/anndata/experimental/merge.py", line 310, in _write_concat_arrays
raise NotImplementedError(
NotImplementedError: Concat of following not supported: ['csc', 'csc']
Please make sure these conditions are met
Report
I was trying to concatenate two large scRNA data set using the concat_on_disk. I confirmed that I have both scRNA data as csr_matrix. But I got the following errors saying 'csc','csc' is not supported, which doesn't make sense. I read the h5ad file into the memory and it is csr. But the concat_on_disk would identify it as csc. Could you please provide some hint what might be wrong here?
Code:
Traceback:
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