Coverage for binette/contig_manager.py: 100%

1import pyfastx 

2from typing import Dict, Iterable, Tuple, Set, Any, Union 

3 

4 

5def parse_fasta_file(fasta_file: str, index_file: str) -> pyfastx.Fasta: 

6 """ 

7 Parse a FASTA file and return a pyfastx.Fasta object. 

8 

9 :param fasta_file: The path to the FASTA file. 

10 

11 :return: A pyfastx.Fasta object representing the parsed FASTA file. 

12 """ 

13 fa = pyfastx.Fasta(fasta_file, build_index=True, index_file=index_file) 

14 return fa 

15 

16 

17def make_contig_index(contigs: Set[str]) -> Tuple[Dict[str, int], Dict[int, str]]: 

18 """ 

19 Create an index mapping for contigs. 

20 

21 :param contigs: A list of contig names. 

22 

23 :return: A tuple containing the contig index mapping dictionaries (contig_to_index, index_to_contig). 

24 """ 

25 contig_to_index = {contig: index for index, contig in enumerate(contigs)} 

26 index_to_contig = {index: contig for contig, index in contig_to_index.items()} 

27 return contig_to_index, index_to_contig 

28 

29 

30def apply_contig_index( 

31 contig_to_index: Dict[str, int], contig_to_info: Dict[str, Any] 

32) -> Dict[int, Union[Any, Iterable[Any]]]: 

33 """ 

34 Apply the contig index mapping to the contig info dictionary. 

35 

36 :param contig_to_index: A dictionary mapping contig names to their corresponding index. 

37 :param contig_to_info: A dictionary mapping contig names to their associated information. 

38 

39 :return: A dictionary mapping contig indices to their associated information. 

40 """ 

41 return {contig_to_index[contig]: info for contig, info in contig_to_info.items()}