How to use the pyteomics.mzml function in pyteomics

for each in scanFileNumber:
            if each[0] in scanDict.keys():
                scanDict[each[0]].append(int(each[1]))
            else:
                scanDict[each[0]] = [int(each[1])]
        # End of Reading Scans from PSM file
        
        # inputPath = sys.argv[1]
        inputPath = args.msms
        ##outPath = "/".join(sys.argv[3].split("/")[:-1])
        # outPath = sys.argv[3]
        outPath = args.out
        ##outFile = sys.argv[3].split("/")[-1]
        allScanList = []
        # Read all scan numbers using indexedmzML/indexList/index/offset tags
        for k in mzml.read(inputPath).iterfind('indexedmzML/indexList/index/offset'):
            if re.search("scan=(\d+)", k['idRef']):
                a = re.search("scan=(\d+)", k['idRef'])
                allScanList.append(int(a.group(1)))
        allScanList = list(set(allScanList))
        # End of Reading mzML file
        # fraction_name = sys.argv[4]
        fraction_name = args.filestring
        if fraction_name in scanDict.keys():
            scansInList = scanDict[fraction_name]
        else:
            scansInList = []
        scansNotInList = list(set(allScanList) - set(scansInList))
        flag = 0
        if removeORretain == "remove":
            scan2retain = scansNotInList
            scan2retain = list(set(scan2retain))

from .metadata.sample import Sample
from .metadata.scan_traits import FAIMS_compensation_voltage, ION_MOBILITY_TYPES
from .xml_reader import (
    XMLReaderBase, iterparse_until,
    get_tag_attributes, _find_section, in_minutes)


def _open_if_not_file(obj, mode='rt'):
    if obj is None:
        return obj
    if hasattr(obj, 'read'):
        return obj
    return open(obj, mode)


class _MzMLParser(mzml.MzML):
    # we do not care about chromatograms
    _indexed_tags = {'spectrum', }

    def __init__(self, *args, **kwargs):
        self._index_file_obj = _open_if_not_file(kwargs.pop("index_file", None))
        super(_MzMLParser, self).__init__(*args, **kwargs)

    def _handle_param(self, element, **kwargs):
        try:
            element.attrib["value"]
        except KeyError:
            element.attrib["value"] = ""
        return super(_MzMLParser, self)._handle_param(element, **kwargs)

    def _determine_array_dtype(self, info):
        dtype = None