[BUG]ERROR - Expression matrix should be provided in the loom file format.

[huangtao-china]

pyscenic aucell \

--num_workers 60
--output sce_SCENIC.loom
input_new.loom
sce.regulons.csv

def twobit_1hamming(twobit: int, size: int) -> List[int]:

2024-12-16 19:56:55,824 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2024-12-16 19:56:56,330 - pyscenic.cli.pyscenic - INFO - Loading gene signatures.
Create regulons from a dataframe of enriched features.
Additional columns saved: []

2024-12-16 19:57:01,899 - pyscenic.cli.pyscenic - INFO - Calculating cellular enrichment.

2024-12-16 19:57:09,334 - pyscenic.cli.pyscenic - INFO - Writing results to file.

2024-12-16 19:58:04,119 - pyscenic.cli.pyscenic - ERROR - Expression matrix should be provided in the loom file format.

[robertzeibich]

Hi @huangtao-china,

Are you still working with pyscenic? You could try the following:

from pyscenic.cli.utils import load_signatures
from pyscenic.aucell import aucell
signatures = load_signatures(f'{name}-reg.csv')
ex_mtx = pd.DataFrame(adata.X.toarray(),index=adata.obs_names, columns=adata.var_names)
auc_mtx = aucell(ex_mtx,signatures,num_workers=24)

The loom file you use as input must be generated by pyscenic/must have the pyscenic format. Is that the case?