fixed trf filtering (102d1d7c) · Commits · Matej Lexa / nested

nested/core/executor.py

0 → 100644

+19 −0

Original line number	Original line	Diff line number	Diff line
			#!/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]:]
			No newline at end of file

nested/core/nester.py

+6 −3

Original line number	Original line	Diff line number	Diff line
	@@ -8,10 +8,11 @@ from nested.core.nested_element import NestedElement
	from nested.core.solo_ltrs import SoloLtrs		from nested.core.solo_ltrs import SoloLtrs
	from nested.logging.logger import NesterLogger		from nested.logging.logger import NesterLogger
	from nested.config.config import config		from nested.config.config import config
			from nested.core.tool_interface import ToolInterface
	import nested.core.tandem_repeat as tandemRepeatFinder		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		"""Class represent nesting in sequence, recursivelly find best evaluated transposon and crop it until no new transposons found

	Attributes:		Attributes:
	@@ -42,7 +43,9 @@ class Nester(object):

	nested_list += self._get_unexpanded_transposon_list(cropped_sequence, self.threshold) # find list of nested transposons		nested_list += self._get_unexpanded_transposon_list(cropped_sequence, self.threshold) # find list of nested transposons
	nested_list = self._expand_transposon_list(nested_list)		nested_list = self._expand_transposon_list(nested_list)
			print(len(nested_list))
	nested_list = self._filter_nested_list(nested_list)		nested_list = self._filter_nested_list(nested_list)
			print(len(nested_list))
	self.nested_element = NestedElement(self.seqid, self.sequence, nested_list)		self.nested_element = NestedElement(self.seqid, self.sequence, nested_list)

	def _get_unexpanded_transposon_list(self, sequence, threshold):		def _get_unexpanded_transposon_list(self, sequence, threshold):

nested/core/tandem_repeat.py

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -11,7 +11,7 @@ from nested.utils import intervals

	class TandemRepeat(TE):		class TandemRepeat(TE):
	def __init__(self, loc, period_size, copies, matches, indels, scor, entropy, monomer):		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.matches = matches
	self.indels = indels		self.indels = indels
	self.entropy = entropy		self.entropy = entropy

nested/core/tool_interface.py

0 → 100644

+8 −0

Original line number	Original line	Diff line number	Diff line
			#!/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
			No newline at end of file

nested/core/tools/init.py

0 → 100644

+0 −0

Empty file added.