Working with splice variant entries in UniProt XML about mzlib HOT 2 OPEN

def get_splice_variants(entry: ET.Element) -> dict:
    """
    Extracts splice variants from the provided UniProt entry.

    Args:
        entry (Element): An Element object representing a UniProt entry.

    Returns:
        dict: A dictionary mapping isoform IDs to lists of tuples containing variation ID, start, and end positions.
    """
    splice_variants = {}

    comment_xpath = '{http://uniprot.org/uniprot}comment[@type="alternative products"]'
    isoform_xpath = '{http://uniprot.org/uniprot}isoform'
    id_xpath = '{http://uniprot.org/uniprot}id'
    seq_xpath = '{http://uniprot.org/uniprot}sequence'

    for comment in entry.findall(comment_xpath):
        for isoform in comment.findall(isoform_xpath):
            isoform_id = isoform.findtext(id_xpath)
            refs = isoform.find(seq_xpath).get('ref')
            if refs:
                refs = refs.split()
                variant_info = []
                for ref in refs:
                    variant = entry.find("{http://uniprot.org/uniprot}feature[@type='splice variant'][@id='" + ref + "']")
                    if variant is not None:
                        description = variant.attrib.get("description")
                        location = variant.find('{http://uniprot.org/uniprot}location')
                        original = variant.find("{http://uniprot.org/uniprot}original")
                        variation = variant.find("{http://uniprot.org/uniprot}variation")
                        if original is not None and variation is not None:
                            original = original.text
                            variation = variation.text
                        start = location.find('{http://uniprot.org/uniprot}begin')
                        end = location.find('{http://uniprot.org/uniprot}end')
                        if start is None:
                            start = int(location.find('{http://uniprot.org/uniprot}position').attrib['position']) - 1
                            end = start
                        else:
                            start = int(start.attrib.get('position', None)) - 1
                            end = int(end.attrib.get('position', None))
                        variant_info.append((ref, description, start, end, original, variation))
                if variant_info:
                    splice_variants[isoform_id] = variant_info

    return splice_variants
    
def apply_splice_variants(sequence: str, refs: List[Tuple[str, str, int, int, str, str]]) -> str:
    """
    Applies the given splice variants to the given sequence.

    Args:
        sequence (str): The sequence to apply the splice variants to.
        refs (List[Tuple[str, str, int, int, str, str]]): A list of tuples containing variation ID, start, and end positions.

    Returns:
        str: The modified sequence with the splice variants applied.
    """
    for ref in sorted(refs, key=lambda x: x[3], reverse=True):  # Apply splice variants with later positions first
        ref_id, description, start, end, original, variation = ref
        if variation is not None:
            sequence = sequence[:start] + variation + sequence[end:]
        else:
            sequence = sequence[:start] + sequence[end:]
    return sequence