CI
cd5554d22f
Build pipeline: vsh-ci-build-template-k4qzr
Source commit: 173327cc56
Source message: Cellranger multi conversion: fix combined AB + CB probe experiments (#1062)
25 lines
738 B
Python
25 lines
738 B
Python
import anndata as ad
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import re
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def set_var_index(adata: ad.AnnData, var_name: str | None = None) -> ad.AnnData:
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"""Sanitize gene names and set the index of the .var DataFrame.
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Parameters
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----------
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adata : AnnData
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Annotated data object
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var_name : str | None
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Name of the column in `adata.var` that contains the gene names, if None, the existing index will be sanitized but not replaced.
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Returns
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-------
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AnnData
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Copy of `adata` with sanitized and replaced index
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"""
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if var_name:
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adata.var.index = [re.sub("\\.[0-9]+$", "", s) for s in adata.var[var_name]]
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else:
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adata.var.index = [re.sub("\\.[0-9]+$", "", s) for s in adata.var.index]
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return adata
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