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fix steinbock missing var column
1 parent 19b6cbf commit 4decbad

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Lines changed: 5 additions & 3 deletions

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src/spatialdata_io/readers/steinbock.py

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -87,9 +87,11 @@ def steinbock(
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# duplicate of adata.obs['image']
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del adata.obs["Image"]
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# / is an invalid character
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adata.var["Final Concentration"] = adata.var["Final Concentration / Dilution"]
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del adata.var["Final Concentration / Dilution"]
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# for backwards compatibility with the demo dataset from spatialdata-io
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if "Final Concentration / Dilution" in adata.var.columns:
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# / is an invalid character
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adata.var["Final Concentration"] = adata.var["Final Concentration / Dilution"]
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del adata.var["Final Concentration / Dilution"]
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# replace all spaces with underscores
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adata.var.columns = adata.var.columns.str.replace(" ", "_")

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