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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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[BUG]pyscenic aucell generated totally same loom file as the input loom, but can be correct if "csv" #459

Open KOBE24DUNK opened 1 year ago

KOBE24DUNK commented 1 year ago

Hi, I've tried the whole pyscenic workflow several times, but every time on the step3 - 'pyscenic aucell' I would encounter this bug:

pyscenic aucell \
    /home/aj186/10X_oJIA_v3_re-analysis/SF_Teff+Treg/data/3_integrated_Seurat_SF_Teff+Treg_filtered.loom \
    $res_dir/3A_integrated_SF_Teff+Treg_pySCENIC_CTX_regulons.csv \
    --output $res_dir/3A_integrated_SF_Teff+Treg_2022-05-16_pySCENIC_filtered.loom \
    --num_workers 20

If I set the output extension as csv, then I would get the right Regulon_AUC.csv file; but if I set it as loom (like above), then the CLI will feed back to me a totally same loom file as the input loom file. It was so strange. Now I hope to have this output.loom to generate a series of plots by running "add.visualization.py". Any suggestions will be much appreciated.

KOBE24DUNK commented 1 year ago

For example, if I set the --output .loom, then the pyscenic aucell will generate totally same loom file as my input file - what it does is only to copy and paste the input loom file. But if I set the --output .csv, then I will get correct [regulonAUC].csv output. It is strange, right? I'm not sure where I made mistakes. In order to run "add.visualization.py", I hope to have a correct output of loom file here.

FourAlarmFire commented 8 months ago

I just realised the size of my output loom file is the same to original loom file too. You mean the file content is the same, right?

xgqyoung commented 8 months ago

The size may not be decisive and I didn't check the content. But my same size output contain no regulon data. Try differente pandas vervsions may help. Because there was a panadas attributed error when the same size loom was generated.

Guiqiyang Xiang

@. | ---- Replied Message ---- | From | @.> | | Date | 3/7/2024 17:26 | | To | @.> | | Cc | @.> , @.***> | | Subject | Re: [aertslab/pySCENIC] [BUG]pyscenic aucell generated totally same loom file as the input loom, but can be correct if "csv" (Issue #459) |

I just realised the size of my output loom file is the same to original loom file too. You mean the file content is the same, right?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

FourAlarmFire commented 8 months ago

The size may not be decisive and I didn't check the content. But my same size output contain no regulon data. Try differente pandas vervsions may help. Because there was a panadas attributed error when the same size loom was generated. | | Guiqiyang Xiang | | @. | ---- Replied Message ---- | From | @.> | | Date | 3/7/2024 17:26 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [aertslab/pySCENIC] [BUG]pyscenic aucell generated totally same loom file as the input loom, but can be correct if "csv" (Issue #459) | I just realised the size of my output loom file is the same to original loom file too. You mean the file content is the same, right? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.>

I just met this error:

Error in get_regulons(sce_SCENIC_test2, column.attr.name = "Regulons") : The attribute 'Regulons' is not available in this loom file. The loom doesn't contain regulon information.

when i code regulons_incidMat_test2 <- get_regulons(sce_SCENIC_test2, column.attr.name="Regulons")

I think is the issue thanks!