def get_relevant_v38_coordinates(self) -> Optional[Set[GeneCoordinate]]: # Returns None if missing some information to determine these coordinates if self.start_coordinate_v38 is None or self.reference_allele_v38 is None: return None else: return get_covered_coordinates(self.start_coordinate_v38, self.reference_allele_v38)
def test_get_covered_coordinates_multiple(self) -> None: start_coordinate = GeneCoordinate("X", 17) result = get_covered_coordinates(start_coordinate, "AGTA") result_expected = { GeneCoordinate("X", 17), GeneCoordinate("X", 18), GeneCoordinate("X", 19), GeneCoordinate("X", 20), } self.assertEqual(result_expected, result)
def get_relevant_coordinates(self) -> Set[GeneCoordinate]: return get_covered_coordinates(self.start_coordinate, self.reference_allele)
def get_relevant_coordinates(self, reference_assembly: ReferenceAssembly) -> Set[GeneCoordinate]: start_coordinate = self.get_start_coordinate(reference_assembly) reference_allele = self.get_reference_allele(reference_assembly) return get_covered_coordinates(start_coordinate, reference_allele)
def test_get_covered_coordinates_single(self) -> None: start_coordinate = GeneCoordinate("X", 17) result = get_covered_coordinates(start_coordinate, "A") result_expected = {start_coordinate} self.assertEqual(result_expected, result)
def test_get_covered_coordinates_empty(self) -> None: start_coordinate = GeneCoordinate("X", 17) result = get_covered_coordinates(start_coordinate, "") result_expected: Set[GeneCoordinate] = set() self.assertEqual(result_expected, result)