import qgis
from qgis.core import *
from qgis.core import QgsApplication
from qgis.core import QgsProject
from qgis.core import QgsProcessingFeedback
from qgis.core import QgsVectorLayer
from qgis.analysis import QgsNativeAlgorithms
import processing
from processing.core.Processing import Processing

path_qgis_installation = "C:/OSGeo4W64/apps/qgis"
QgsApplication.setPrefixPath(path_qgis_installation, True)

qgs = QgsApplication([], False)
qgs.initQgis()

QgsApplication.processingRegistry().addProvider(QgsNativeAlgorithms())
Processing.initialize()

input_file = QgsVectorLayer('.../file_name.shp')
overlay_file = QgsVectorLayer('.../file_name.shp')
output_fil = '.../file_name.shp'

processing.run(
    "native:clip",
    {
        'INPUT':input_file,
        'OVERLAY':overlay_file,
        'OUTPUT':output_fil
    }
)

qgs.exitQgis()