modules: added mite filtering; delete tmp files at the end

import os

import click

import glob

import shutil

from concurrent import futures

from datetime import datetime

from subprocess import CalledProcessError

        process_sequence(sequence, sketcher, sketch, format, output_fasta_offset, output_folder,

                         initial_threshold, threshold_multiplier, number_of_errors,

                         dependency_resolver)

    shutil.rmtree("/tmp/nested/")

    end_time = datetime.now()

    print('Total time: {}'.format(end_time - start_time))

    print('Number of errors: {}'.format(number_of_errors[0]))

class ToolInterface:

    def __init__(self, sequence: SeqRecord):

        self.output_object: Type[BaseOutputObject]

        self.output_object: BaseOutputObject = None

        self.sequence: Seq = sequence.seq

        self.seqId: str = sequence.id

from nested.entities.mite import Mite

from nested.output.output_objects.mite_output_object import MiteOutputObject

from nested.config.config import config, args_dict_to_list

from nested.utils import intervals

class MiteFinder(ToolInterface):

        stdout, stderr = process.communicate()

        mites = self._get_mites()

        candidates = self._get_mites()

        mites = self._filter_candidates(candidates)

        mites.sort(key=lambda e: e.location[0], reverse=True)

        self.output_object = MiteOutputObject(self.seqId, sequence, mites)

        return mites

            element = Mite(location, score, tir_left, tir_right)

            result.append(element)

        result.sort(key=lambda e: e.location[0], reverse=True)

        return result

    def _filter_candidates(self, candidates: List[Mite]) -> List[Mite]:

        mites = []

        candidates.sort(key=lambda e: e.score, reverse=True)

        for candidate in candidates:

            add = True

            for mite in mites:

                if candidate.location == mite.location:

                    continue

                if intervals.intersect(mite.location, candidate.location):

                    add = False

                    break

            if add:

                mites.append(candidate)

        return mites