INNER CODE UNIT · Python

find_chain_file

hillerlab/TOGA · CESAR_wrapper.py:367

def find_chain_file(ref_name, chain_arg):
    """Return chain file path."""
    if os.path.isfile(chain_arg):
        # not an alias -> just return it
        return chain_arg
    # not a chain path/ Hillerlab-specific place!
    chain_path = chain_alias_template.format(ref_name, chain_arg)
    die(
        f"Error! File {chain_path} not found! Please set the chain path explicitly.", 1
    ) if not os.path.isfile(chain_path) else None
    return chain_path


def get_exons(bed_data, t_db):
    """Extract exons sequences for reference."""
    exons_raw = (
        bed_data["blocks"][::-1] if not bed_data["strand"] else bed_data["blocks"]
    )

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