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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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Error converting loom to anndata #34

Open Vinayaksiv-17 opened 3 years ago

Vinayaksiv-17 commented 3 years ago

I tried converting loom to anndata and it is giving the following error.

`sceasy::convertFormat('/home/user/Documents/brain_scRNA/embryonic_brain_merged/dev_all.loom', from="loom", to="anndata", outFile='embroynic.h5ad')
Warning: anndata <0.6.20 detected. Upgrade to handle multi-dimensional embeddings.
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  OSError: Unable to create file (unable to open file: name = '/home/user/Documents/brain_scRNA/embryonic_brain_merged/dev_all.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Detailed traceback:
  File "/home/user/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/anndata/readwrite/read.py", line 157, in read_loom
    with connect(filename, 'r', **kwargs) as lc:
  File "/home/user/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/loompy/loompy.py", line 1140, in connect
    return LoomConnection(filename, mode, validate=validate, spec_version=spec_version)
  File "/home/user/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/loompy/loompy.py", line 83, in __init__
    if not lv.validate(filename):
  File "/home/user/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/loompy/loom_validator.py", line 48, in validate
    with h5py.File(path) as f:
  File "/home/user/.local/s`