Coverage for src/python/ensembl/io/genomio/gff3/features.py: 84%

1# See the NOTICE file distributed with this work for additional information 

2# regarding copyright ownership. 

3# 

4# Licensed under the Apache License, Version 2.0 (the "License"); 

5# you may not use this file except in compliance with the License. 

6# You may obtain a copy of the License at 

7# 

8# http://www.apache.org/licenses/LICENSE-2.0 

9# 

10# Unless required by applicable law or agreed to in writing, software 

11# distributed under the License is distributed on an "AS IS" BASIS, 

12# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 

13# See the License for the specific language governing permissions and 

14# limitations under the License. 

15"""GFF3 features.""" 

16 

17from __future__ import annotations 

18 

19__all__ = [ 

20 "GFFSeqFeature", 

21] 

22 

23from Bio.SeqFeature import SeqFeature, Location 

24 

25 

26class GFFSeqFeature(SeqFeature): 

27 """Extends `Bio.SeqFeature.SeqFeature` with sub_features, to be used for typing.""" 

28 

29 def __init__( 

30 self, 

31 location: Location | None = None, 

32 *, 

33 type: str = "", # pylint: disable=W0622 

34 id: str = "<unknown id>", # pylint: disable=W0622 

35 qualifiers: dict | None = None, 

36 sub_features: list[GFFSeqFeature] | None = None, 

37 ): 

38 super().__init__(location, type=type, id=id, qualifiers=qualifiers) 

39 if sub_features is None: 39 ↛ 41line 39 didn't jump to line 41 because the condition on line 39 was always true

40 sub_features = [] 

41 self.sub_features = sub_features 

42 

43 @classmethod 

44 def cast(cls, feat: SeqFeature) -> GFFSeqFeature: 

45 """Cast a SeqFeature to a GFFSeqFeature.""" 

46 feat.__class__ = cls 

47 if not hasattr(feat, "sub_features"): 47 ↛ 48line 47 didn't jump to line 48 because the condition on line 47 was never true

48 feat.sub_features = [] # type: ignore[attr-defined] 

49 return feat # type: ignore[return-value]