pyproject.toml

@@ -13,7 +13,6 @@ dependencies = [
 ]
 requires-python = ">=3.12"
 description = "A library to rapidly fetch fetch MLST profiles given sequences for various diseases."
-license = {text = "GPL-3.0-or-later"}
 
 [project.urls]
 Homepage = "https://github.com/Syph-and-VPD-Lab/autoBIGS.engine"

src/autobigs/engine/analysis/bigsdb.py

@@ -124,17 +124,13 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
 
     async def profile_multiple_strings(self, query_named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]:
         async for named_strings in query_named_string_groups:
-            names: list[str] = list()
-            sequences: list[str] = list()
             for named_string in named_strings:
-                names.append(named_string.name)
+                try:
-                sequences.append(named_string.sequence)
+                    yield NamedMLSTProfile(named_string.name, (await self.profile_string([named_string.sequence])))
-            try:
+                except NoBIGSdbMatchesException as e:
-                yield NamedMLSTProfile("-".join(names), (await self.profile_string(sequences)))
+                    if stop_on_fail:
-            except NoBIGSdbMatchesException as e:
+                        raise e
-                if stop_on_fail:
+                    yield NamedMLSTProfile(named_string.name, None)
-                    raise e
-                yield NamedMLSTProfile("-".join(names), None)
 
     async def close(self):
         await self._http_client.close()

src/autobigs/engine/writing.py

@@ -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, NamedMLSTProfile
+from autobigs.engine.structures.mlst import Allele, MLSTProfile
 
 
 def alleles_to_text_map(alleles: Collection[Allele]) -> Mapping[str, Union[Sequence[str], str]]:
@@ -17,14 +17,12 @@ 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[NamedMLSTProfile], handle: Union[str, bytes, PathLike[str], PathLike[bytes]]) -> Sequence[str]:
+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]:
     failed = list()
     with open(handle, "w", newline='') as filehandle:
         header = None
         writer: Union[csv.DictWriter, None] = None
-        async for named_mlst_profile in mlst_profiles_iterable:
+        async for name, 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

tests/autobigs/engine/test_writing.py

@@ -3,7 +3,7 @@ from typing import AsyncIterable, Iterable
 import pytest
 from autobigs.engine.structures.alignment import AlignmentStats
 from autobigs.engine.writing import alleles_to_text_map, write_mlst_profiles_as_csv
-from autobigs.engine.structures.mlst import Allele, MLSTProfile, NamedMLSTProfile
+from autobigs.engine.structures.mlst import Allele, MLSTProfile
 import tempfile
 from csv import reader
 from os import path
@@ -11,20 +11,20 @@ from os import path
 
 @pytest.fixture
 def dummy_alphabet_mlst_profile():
-    return NamedMLSTProfile("name", MLSTProfile((
+    return MLSTProfile((
         Allele("A", "1", None),
         Allele("D", "1", None),
         Allele("B", "1", None),
         Allele("C", "1", None),
         Allele("C", "2", AlignmentStats(90, 10, 0, 90))
-    ), "mysterious", "very mysterious"))
+    ), "mysterious", "very mysterious")
 
 async def iterable_to_asynciterable(iterable: Iterable):
     for iterated in iterable:
         yield iterated
 
 async def test_column_order_is_same_as_expected_file(dummy_alphabet_mlst_profile: MLSTProfile):
-    dummy_profiles = [dummy_alphabet_mlst_profile]
+    dummy_profiles = [("test_1", dummy_alphabet_mlst_profile)]
     with tempfile.TemporaryDirectory() as temp_dir:
         output_path = path.join(temp_dir, "out.csv")
         await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
@@ -34,8 +34,8 @@ async def test_column_order_is_same_as_expected_file(dummy_alphabet_mlst_profile
             target_columns = lines[4:]
             assert target_columns == sorted(target_columns)
 
-async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profile: NamedMLSTProfile):
+async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profile: MLSTProfile):
-    mapping = alleles_to_text_map(dummy_alphabet_mlst_profile.mlst_profile.alleles) # type: ignore
+    mapping = alleles_to_text_map(dummy_alphabet_mlst_profile.alleles)
     expected_mapping = {
         "A": "1",
         "B": "1",