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)