infercnvpy.io.genomic_position_from_gtf

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 | str) – Path to the GTF file

  • adata (Optional[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 (Literal['gene_id', 'gene_name'] (default: 'gene_name')) – Use this GTF column to match it to anndata

  • adata_gene_id (Optional[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 | None

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