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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 import asyncio
from io import TextIOWrapper from io import TextIOWrapper
from os import path
from typing import Any, AsyncGenerator, Iterable, Union from typing import Any, AsyncGenerator, Iterable, Union
from Bio import SeqIO 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") fasta_sequences = asyncio.to_thread(SeqIO.parse, handle=handle, format="fasta")
results = [] results = []
for fasta_sequence in await fasta_sequences: 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 return results
async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[Iterable[NamedString], Any]: async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[Iterable[NamedString], Any]: