infercnvpy.io.genomic_position_from_gtf

infercnvpy.io.genomic_position_from_gtf(gtf_file, adata=None, *, gtf_gene_id='gene_name', adata_gene_id=None, inplace=True)

Get genomic gene positions from a GTF file.

The GTF file needs to match the genome annotation used for your single cell dataset.

Warning

Currently only tested with GENCODE GTFs.

Parameters

gtf_file : Path | strUnion[Path, str]

Path to the GTF file

adata : AnnData | NoneOptional[AnnData] (default: None)

Adds the genomic positions to adata.var. If adata is None, returns a data frame with the genomic positions instead.

gtf_gene_id : {‘gene_id’, ‘gene_name’}Literal[‘gene_id’, ‘gene_name’] (default: 'gene_name')

Use this GTF column to match it to anndata

adata_gene_id : str | NoneOptional[str] (default: None)

Match this column to the gene ids from the GTF file. Default: use adata.var_names.

inplace : bool (default: True)

If True, add the annotations directly to adata, otherwise return a dataframe.

Return type

DataFrame | NoneOptional[DataFrame]