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conversion of collection of alleles to map now produces results with tuples instead of lists

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Harrison Deng 2025-02-12 16:36:31 +00:00
parent 4183840ba0
commit ba606c35a9
1 changed files with 3 additions and 1 deletions
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src/autobigs/engine/writing.py
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@ -6,13 +6,15 @@ from typing import AsyncIterable, Collection, Mapping, Sequence, Union
from autobigs.engine.structures.mlst import Allele, MLSTProfile
def alleles_to_text_map(alleles: Collection[Allele]) -> Mapping[str, Union[list[str], str]]:
def alleles_to_text_map(alleles: Collection[Allele]) -> Mapping[str, Union[Sequence[str], str]]:
result = defaultdict(list)
for allele in alleles:
result[allele.allele_locus].append(allele.allele_variant + ("*" if allele.partial_match_profile is not None else ""))
for locus in result.keys():
if len(result[locus]) == 1:
result[locus] = result[locus][0] # Take the only one
else:
result[locus] = tuple(result[locus]) # type: ignore
return dict(result)
async def write_mlst_profiles_as_csv(mlst_profiles_iterable: AsyncIterable[tuple[str, Union[MLSTProfile, None]]], handle: Union[str, bytes, PathLike[str], PathLike[bytes]]) -> Sequence[str]: