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Fix dsb background #314

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merged 3 commits into from
Nov 27, 2024
Merged

Fix dsb background #314

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6f87e72
Update run_preprocess_prot.py
wlason Oct 15, 2024
6ea37e9
check dsb bg obj in run_preprocess_prot.py
wlason Oct 15, 2024
5dda110
fix typo in run_preprocess_prot.py
wlason Oct 16, 2024
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11 changes: 11 additions & 0 deletions panpipes/python_scripts/run_preprocess_prot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,17 @@
else:
L.error("You must specify a background MuData to run dsb, containing both rna and prot")
sys.exit("You must specify a background MuData to run dsb, containing both rna and prot")

# RNA and PROT layer must be present in the object to run dsb
if 'rna' not in list(all_mdata_bg.mod.keys()):
L.error("The MuData you specified does not contain rna modality. Cannot run dsb")
sys.exit("The MuData you specified does not contain rna modality. Cannot run dsb")

# the RNA and PROT must intersect - they won't if experimental design included some cells without PROT data
L.info("Checking that only cells with PROT signal present are in the background object")
if all_mdata_bg['rna'].shape[0] != all_mdata_bg['prot'].shape[0]:
mu.pp.intersect_obs(mdata_bg)
all_mdata_bg.update()

# checking that the same proteins are in foreground and background (since foreground might have been filtered)
L.info("Checking that the same proteins are in foreground and background")
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