fixed trf filtering

#!/usr/bin/env python3

from nested.core.nester import Nester

from nested.core.tandem_repeat import TandemRepeat

from nested.core.tools.tandem_repeat_finder import TandemRepeatFinder

class Executor():

    def __init__(self, sequence):

        self.sequence = sequence

        self.tool_order = [TandemRepeatFinder(), Nester()]

    def run_main_loop(self):

        elements = []

        for tool in self.tool_order:

            elements += tool.run(self.sequence)

    def _crop_sequence(self, elements):

        for element in elements:

            self.sequence = self.sequence[:element.location[0]] + self.sequence[element.location[1]:]

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from nested.core.solo_ltrs import SoloLtrs

from nested.logging.logger import NesterLogger

from nested.config.config import config

from nested.core.tool_interface import ToolInterface

import nested.core.tandem_repeat as tandemRepeatFinder

class Nester(object):

class Nester(ToolInterface):

    """Class represent nesting in sequence, recursivelly find best evaluated transposon and crop it until no new transposons found

    Attributes:

        nested_list += self._get_unexpanded_transposon_list(cropped_sequence, self.threshold)  # find list of nested transposons

        nested_list = self._expand_transposon_list(nested_list)

        print(len(nested_list))

        nested_list = self._filter_nested_list(nested_list)

        print(len(nested_list))       

        self.nested_element = NestedElement(self.seqid, self.sequence, nested_list)

    def _get_unexpanded_transposon_list(self, sequence, threshold):

class TandemRepeat(TE):

    def __init__(self, loc, period_size, copies, matches, indels, scor, entropy, monomer):

        super().__init__(location=loc, score=scor)

        super().__init__(location=loc, score=scor, ltr_left_location=[float('nan'), float('nan')])

        self.matches = matches

        self.indels = indels

        self.entropy = entropy

#!/usr/bin/env python3

class ToolInterface():

    def run(self, sequence):

        """Runs selected tool, if any arguments are needed they are taken from config.yml or constructor

        Returns: collection of BaseElement

        """        

        pass

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