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Fix steinbock missing var column #307

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Merged
LucaMarconato merged 1 commit into from
May 25, 2025
Merged

Fix steinbock missing var column #307

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8 changes: 5 additions & 3 deletions src/spatialdata_io/readers/steinbock.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,9 +87,11 @@ def steinbock(
# duplicate of adata.obs['image']
del adata.obs["Image"]

# / is an invalid character
adata.var["Final Concentration"] = adata.var["Final Concentration / Dilution"]
del adata.var["Final Concentration / Dilution"]
# for backwards compatibility with the demo dataset from spatialdata-io
if "Final Concentration / Dilution" in adata.var.columns:
# / is an invalid character
adata.var["Final Concentration"] = adata.var["Final Concentration / Dilution"]
del adata.var["Final Concentration / Dilution"]

# replace all spaces with underscores
adata.var.columns = adata.var.columns.str.replace(" ", "_")
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