Changed FASTA reading to group based on file for merging partial targets

src/autobigs/engine/reading.py

@@ -5,12 +5,13 @@ from Bio import SeqIO
 
 from autobigs.engine.structures.genomics import NamedString
 
-async def read_fasta(handle: Union[str, TextIOWrapper]) -> AsyncGenerator[NamedString, Any]:
+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:
-        yield NamedString(fasta_sequence.id, str(fasta_sequence.seq))
+        results.append(NamedString(fasta_sequence.id, str(fasta_sequence.seq)))
+    return results
 
-async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[NamedString, Any]:
+async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[Iterable[NamedString], Any]:
     for handle in handles:
-        async for named_seq in read_fasta(handle):
-            yield named_seq
+        yield await read_fasta(handle)

tests/autobigs/engine/test_reading.py

@@ -2,6 +2,6 @@ from autobigs.engine.reading import read_fasta
 
 
 async def test_fasta_reader_not_none():
-    named_strings = read_fasta("tests/resources/tohama_I_bpertussis.fasta")
-    async for named_string in named_strings:
+    named_strings = await read_fasta("tests/resources/tohama_I_bpertussis.fasta")
+    for named_string in named_strings:
         assert named_string.name == "BX470248.1"