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Added original filename to csv output
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Harrison Deng 2025-03-13 14:17:08 +00:00
parent 3074997db6
commit 62fdada9c1
1 changed files with 2 additions and 1 deletions
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src/autobigs/engine/reading.py
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@ -1,5 +1,6 @@
import asyncio
from io import TextIOWrapper
from os import path
from typing import Any, AsyncGenerator, Iterable, Union
from Bio import SeqIO
@ -9,7 +10,7 @@ async def read_fasta(handle: Union[str, TextIOWrapper]) -> Iterable[NamedString]
fasta_sequences = asyncio.to_thread(SeqIO.parse, handle=handle, format="fasta")
results = []
for fasta_sequence in await fasta_sequences:
results.append(NamedString(fasta_sequence.id, str(fasta_sequence.seq)))
results.append(NamedString("{0}:{1}".format(path.basename(handle.name if isinstance(handle, TextIOWrapper) else handle), fasta_sequence.id), str(fasta_sequence.seq)))
return results
async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[Iterable[NamedString], Any]: