documentation (aef715bc) · Commits · Matej Lexa / nested

nested/core/executor.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -39,4 +39,4 @@ class Executor:
		def _recalculate_coordinates(self, nested_list: List[BaseElement]) -> NoReturn:
		for i in reversed(range(len(nested_list) - 1)):
		for j in range(i + 1, len(nested_list)):
		nested_list[j].recalculate_offset(nested_list[i].location)
		nested_list[j].recalculate_coordinates(nested_list[i].location)

+2 −2

Original line number	Diff line number	Diff line
		@@ -15,9 +15,9 @@ class DiscoveryToolInterface:
		Finds retrotransposons in sequence.
		Args:
		sequence_id: id of the sequence
		sequence: dna sequence
		sequence: DNA sequence

		Returns:
		List[TE]: list of identified retrotransposons
		List of identified retrotransposons
		"""
		pass

+5 −2

Original line number	Diff line number	Diff line
		@@ -16,7 +16,10 @@ class ToolInterface:

		def run(self, sequence: Seq) -> List[BaseElement]:
		"""
		Runs selected tool, if any arguments are needed they are taken from config.yml or constructor
		Returns: List[BaseElement]
		Runs selected tool, if any arguments are needed they are taken from config.yml or class attributes.
		Args:
		sequence: sequence
		Returns:
		List of identified elements.
		"""
		pass

+24 −1

Original line number	Diff line number	Diff line
		@@ -7,6 +7,16 @@ from nested.utils import intervals


		class BaseElement:
		"""
		Class representing identified element in sequence.

		Attributes:
		location: coordinates of the element in format [lower, higher]
		score: score
		type: type of the element in string, should be used as a key in parent element features dictionary
		features: features of the element
		"""

		def __init__(self, location: List[int], score: float,
		element_type: str,
		features: Optional[Dict[str, Union["BaseElement", List["BaseElement"]]]] = None):
		@@ -15,7 +25,12 @@ class BaseElement:
		self.type = element_type
		self.features = features if features is not None else {}

		def recalculate_offset(self, other_location: List[int]) -> NoReturn:
		def recalculate_coordinates(self, other_location: List[int]) -> NoReturn:
		"""
		Recalculates coordinates.
		Args:
		other_location: location of different element
		"""
		self.location = intervals.expand(other_location, self.location)

		for feature in self.features.keys():
		@@ -27,6 +42,14 @@ class BaseElement:

		def try_add_feature(self, name: str, location: List[int], score: float = 0,
		feature_type: Type = None) -> NoReturn:
		"""
		Tries to create new feature and add it to features dictionary.
		Args:
		name: key in features dictionary and type in created feature
		location: location
		score: score
		feature_type: class which should be instantiated
		"""
		if location is None or math.isnan(location[0]):
		return

+10 −9

Original line number	Diff line number	Diff line
		@@ -5,15 +5,16 @@ from nested.entities.base_element import BaseElement


		class DomainDante(BaseElement):
		"""Class representing domain parsed from blastx output.

		Atrributes:
		evalue (float): evalue (same as blastx output)
		frame (tuple): frame (same as blastx output)
		score (float): score (same as blastx output)
		title (str): title (same as blastx output)
		location (list): location [from, to] (from > to for negative strand)
		type (str): type of domain (AP, GAG, INT, ...)
		"""
		Class representing domain parsed from blastx output.

		Attributes:
		evalue: evalue (same as blastx output)
		frame: frame (same as blastx output)
		score: score (same as blastx output)
		title: title (same as blastx output)
		location: location [from, to] (from > to for negative strand)
		type: type of domain (PROT, GAG, INT, ...)
		"""

		def __init__(self, evalue: float = None, frame: Tuple[int] = None,