CI
4caaaf68ef
Build pipeline: openpipelines-bio.openpipeline.v4.0.0-kd9qj
Source commit: de02293c9e
Source message: Bump version to v4.0.0
69 lines
2.1 KiB
Python
69 lines
2.1 KiB
Python
import anndata as ad
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def strip_version_number(gene_series: list[str]) -> list[str]:
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"""Sanitize ensemble ID's by removing version numbers.
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Parameters
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----------
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gene_series : list[str]
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List of ensemble ID's to sanitize.
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Returns
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-------
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list[str]
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List of sanitized ensemble ID's.
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"""
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# Convert to string type to handle Categorical series
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gene_series = gene_series.astype(str)
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# Pattern matches Ensembl IDs: starts with ENS, followed by any characters,
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# then an eleven digit number, optionally followed by .version_number
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ensembl_pattern = r"^(ENS.*\d{11})(?:\.\d+)?$"
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ensembl_mask = gene_series.str.match(ensembl_pattern)
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sanitized = gene_series.where(
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~ensembl_mask, gene_series.str.extract(ensembl_pattern)[0]
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)
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return sanitized
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def set_var_index(
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adata: ad.AnnData, var_name: str | None = None, sanitize_ensembl_ids: bool = True
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) -> ad.AnnData:
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"""Sanitize gene names (optional) 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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sanitize_ensembl_ids : bool
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Whether to sanitize gene names by removing version numbers.
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Returns
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-------
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AnnData
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Copy of `adata` with optionally sanitized and replaced index
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"""
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gene_names = adata.var[var_name] if var_name else adata.var.index.to_series()
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if sanitize_ensembl_ids:
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ori_gene_names = len(gene_names)
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gene_names = strip_version_number(gene_names)
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sanitized_gene_names = len(set(gene_names))
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assert ori_gene_names == sanitized_gene_names, (
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"Sanitizing gene names resulted in duplicated gene names.\n"
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"Please ensure unique gene names before proceeding.\n"
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"Please make sure --var_gene_names contains ensembl IDs (not gene symbols) "
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"when --sanitize_ensembl_ids is set to True."
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)
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adata.var.index = gene_names.astype(str)
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return adata
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