Link pre- and mature given GFF record

link.py

def link_mature_and_pre(pre_dic, mature_dic):
    """
    miR-XXX-3p, miR-XXX-5p (mature) are derives from mir-XXX (pre),
    then it can be linked following:
    {pre: {3p: XXX, 5p: XXX}}
    """

    def matID_to_name(q, mature_HTSeq):
        # MIRAMTXXXX (transcript_id) to miR-XXX-Xp
        matures = []
        for name, attr in mature_HTSeq.items():
            if q == attr.attr["Derives_from"]:
                matures.append(attr.attr["Name"])
        return matures

    def name_to_matID(q, mature_dic):
        # miR-XXX-Xp to MIMATXXXXX (transcript_id)
        for name, attr in mature_dic.items():
            if q == attr.attr["Name"]:
                return attr

    def classify_miRNA(matures, mature_dic):
        """
        Define type of 3p or 5p or '' in mature miRNA

        Args:
         [miR-XXX-3p, miR-XXX-5p]

        Returns:
         {"3p": miR-XXX-3p, "5p": miR-XXX-5p}
        """

        _type = {}
        for mat in matures:
            if re.match(r"^hsa-(:?miR|let)(?:-[\d\w]+)(-3p$)", mat):
                _type["3p"] = name_to_matID(mat, mature_dic)
            elif re.match(r"^hsa-(:?miR|let)(?:-[\d\w]+)(-5p$)", mat):
                _type["5p"] = name_to_matID(mat, mature_dic)
            elif re.match(r"^hsa-(:?miR|let)(?:-[\d\w]+)$", mat):
                _type["unknown"] = name_to_matID(mat, mature_dic)
        return _type

    result = defaultdict(str)
    for pre_id, pre_attr in pre_dic.items():
        if pre_id in [mature_dic[_].attr["Derives_from"] for _ in mature_dic]:
            # link pre and mature
           result[pre_id] = classify_miRNA(matID_to_name(pre_id, mature_dic), mature_dic)
    return result