bedfilegenerator ¶

bedfilegenerator(
    *,
    gene_list: str | list[str],
    bed_file_name: str,
    output_folder: str,
    whole_gene_list: str | list[str] | None,
    ref_folder: str | None = None,
    parsed_gtf_path: str | None = None,
    whole_gene_locs_path: str | None = None,
    cds: bool = False,
)

The main command for the CLI entry point. Generate and sort BED files from a parsed GTF file.

Parameters:

Name	Type	Description	Default
`gene_list`	`str \| list[str]`	List of gene names to include.	required
`bed_file_name`	`str`	Name of the output BED file.	required
`output_folder`	`str`	Folder to save the output BED file.	required
`whole_gene_list`	`str \| list[str] \| None`	List of whole gene names to include.	required
`ref_folder`	`str \| None`	Path to the folder for reference files. e.g "fasta" or "gtf". Will be concatenated with the default paths.	`None`
`parsed_gtf_path`	`str`	Path to Parsed GTF file. e.g "Homo_sapiens.GRCh38.112.parsed.gtf"	`None`
`whole_gene_locs_path`	`str`	Path to whole gene locs file. e.g "Homo_sapiens.GRCh38.112.gtf.gene_names.sorted.cleaned.bed"	`None`
`cds`	`bool`	If True, use CDS features; otherwise use exon features.	`False`