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Writing now uses named MLST profile
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Harrison Deng
2025-02-18 16:03:17 +00:00
parent 5a03c7e8d8
commit 7384895578
2 changed files with 12 additions and 10 deletions
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8
src/autobigs/engine/writing.py
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@@ -3,7 +3,7 @@ import csv
from os import PathLike
from typing import AsyncIterable, Collection, Mapping, Sequence, Union
from autobigs.engine.structures.mlst import Allele, MLSTProfile
from autobigs.engine.structures.mlst import Allele, MLSTProfile, NamedMLSTProfile
def alleles_to_text_map(alleles: Collection[Allele]) -> Mapping[str, Union[Sequence[str], str]]:
@@ -17,12 +17,14 @@ def alleles_to_text_map(alleles: Collection[Allele]) -> Mapping[str, Union[Seque
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]:
async def write_mlst_profiles_as_csv(mlst_profiles_iterable: AsyncIterable[NamedMLSTProfile], handle: Union[str, bytes, PathLike[str], PathLike[bytes]]) -> Sequence[str]:
failed = list()
with open(handle, "w", newline='') as filehandle:
header = None
writer: Union[csv.DictWriter, None] = None
async for name, mlst_profile in mlst_profiles_iterable:
async for named_mlst_profile in mlst_profiles_iterable:
name = named_mlst_profile.name
mlst_profile = named_mlst_profile.mlst_profile
if mlst_profile is None:
failed.append(name)
continue