Coverage for src/python/ensembl/io/genomio/seq_region/mappings.py: 100%

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"""Seq region mappings.""" 

16 

17__all__ = [ 

18 "SYNONYM_MAP", 

19 "MOLECULE_LOCATION", 

20 "LOCATION_CODON", 

21] 

22 

23from types import MappingProxyType 

24from typing import Mapping 

25 

26 

27SYNONYM_MAP: Mapping[str, str] = MappingProxyType( 

28 { 

29 "Assigned-Molecule": "INSDC", 

30 "GenBank-Accn": "GenBank", 

31 "RefSeq-Accn": "RefSeq", 

32 "Sequence-Name": "INSDC_submitted_name", 

33 } 

34) 

35MOLECULE_LOCATION: Mapping[str, str] = MappingProxyType( 

36 { 

37 "apicoplast": "apicoplast_chromosome", 

38 "chromosome": "nuclear_chromosome", 

39 "kinetoplast": "kinetoplast_chromosome", 

40 "linkage group": "linkage_group", 

41 "mitochondrion": "mitochondrial_chromosome", 

42 "plasmid": "plasmid", 

43 } 

44) 

45LOCATION_CODON: Mapping[str, int] = MappingProxyType({"apicoplast_chromosome": 4})