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Antoine #8

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merged 2 commits into from
Aug 27, 2024
Merged

Antoine #8

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d127462
Merge
AntoinePassemiers Aug 26, 2024
0775229
Scenicplus: change output location
AntoinePassemiers Aug 26, 2024
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17 changes: 2 additions & 15 deletions src/methods/multi_omics/scenicplus/script.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,10 @@

## VIASH START
par = {
<<<<<<< HEAD
'multiomics_rna': '/base/resources/resources_test/grn-benchmark/multiomics_rna.h5ad',
'multiomics_atac': '/base/resources/resources_test/grn-benchmark/multiomics_atac.h5ad',
'temp_dir': '/base/output/scenicplus',
'pycistopic_object': '/base/output/scenicplus/pycistopic.pkl',
'cistopic_object': '/base/output/scenicplus/pycistopic.pkl',
'prediction': '/base/output/prediction.csv',
'qc': False,
'num_workers': 4
Expand Down Expand Up @@ -346,7 +345,7 @@

# LDA-based topic modeling
print('Run LDA models')
if not os.path.exists(par['pycistopic_object']):
if not os.path.exists(par['cistopic_object']):

# Topic modeling
n_topics = [2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50]
Expand Down Expand Up @@ -570,18 +569,6 @@

work_dir = os.path.join(out_dir, 'scenicplus')
os.makedirs(work_dir, exist_ok=True)
=======
'multiomics_rna': 'resources/grn-benchmark/multiomics_rna.h5ad',
'multiomics_atac': 'resources/grn-benchmark/multiomics_atac.h5ad',
'temp_dir': 'output/scenicplus',
'prediction': 'output/prediction.csv',
}
## VIASH END

work_dir = par['temp_dir']
par['cistopic_out'] = f'{work_dir}/cistopic_out'
par['cistopic_object'] = os.path.join(par['cistopic_out'], f'cistopic_object_with_model.pkl')
>>>>>>> dbe05111aa79f6bc2da8a8f0f10f06d8192b7bc4
os.makedirs(os.path.join(work_dir, 'scRNA'), exist_ok=True)

# Download databases
Expand Down
4 changes: 2 additions & 2 deletions src/methods/multi_omics/scenicplus/test.sh
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
#viash build src/methods/multi_omics/scenicplus/config.novsh.yaml --platform docker -o bin/scenicplus && bin/scenicplus/scenicplus --multiomics_atac resources/resources_test/grn-benchmark/multiomics_atac.h5ad --multiomics_rna resources/resources_test/grn-benchmark/multiomics_rna.h5ad --temp_dir output/scenicplus --prediction output/scenicplus/prediction.csv --pycistopic_object output/scenicplus/pycistopic.pkl
docker run -v /mnt/c/Users/antoi/git/task_grn_inference/:/base apassemi/scenicplus python /base/src/methods/multi_omics/scenicplus/script.py
viash build src/methods/multi_omics/scenicplus/config.vsh.yaml --platform docker -o bin/scenicplus && bin/scenicplus/scenicplus --multiomics_atac resources/resources_test/grn-benchmark/multiomics_atac.h5ad --multiomics_rna resources/resources_test/grn-benchmark/multiomics_rna.h5ad --temp_dir output/scenicplus --prediction output/scenicplus/prediction.csv --cistopic_object output/scenicplus/pycistopic.pkl
#docker run -v /mnt/c/Users/antoi/git/task_grn_inference/:/base apassemi/scenicplus python /base/src/methods/multi_omics/scenicplus/script.py
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