Added original filename to csv output

autobigs-engine/meta.yaml

@@ -1,44 +0,0 @@
-{% set name = "autoBIGS.engine" %}
-{% set version = "0.12.1.dev1+gb8cebb8.d20250221" %}
-
-package:
-  name: {{ name|lower|replace(".", "-") }}
-  version: {{ version }}
-
-source:
-  url: file:///workspaces/autoBIGS.engine/dist/autobigs_engine-0.12.1.dev1%2Bgb8cebb8.d20250221.tar.gz
-  sha256: c86441b94f935cfa414ff28ca4c026a070e0fb15988ea3bb7d1a942859a09b16
-
-build:
-  noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 0
-  run_exports:
-    - {{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}
-requirements:
-  host:
-    - python >=3.12
-    - setuptools >=64
-    - setuptools-scm >=8
-    - pip
-  run:
-    - python >=3.12
-    - biopython ==1.85
-    - aiohttp ==3.11.*
-
-test:
-  imports:
-    - autobigs
-  commands:
-    - pip check
-  requires:
-    - pip
-
-about:
-  summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
-  license: GPL-3.0-or-later
-  license_file: LICENSE
-  home: https://github.com/Syph-and-VPD-Lab/autoBIGS.engine
-extra:
-  recipe-maintainers:
-    - Harrison Deng

src/autobigs/engine/reading.py

@@ -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]: