Added additional test for fully automatic typing based on sequence

src/automlst/cli/aggregated.py

@@ -1,6 +1,6 @@
 from os import path
 from typing import Any, AsyncGenerator, AsyncIterable, Iterable, Sequence
-from automlst.engine.data.MLST import MLSTProfile
+from automlst.engine.data.mlst import MLSTProfile
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.local.abif import read_abif
 from automlst.engine.local.fasta import read_fasta

src/automlst/engine/local/csv.py

@@ -3,7 +3,7 @@ from io import TextIOWrapper
 from os import PathLike
 from typing import AsyncIterable, Iterable, Mapping, Sequence, Union
 
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 
 
 def loci_alleles_variants_from_loci(alleles_map: Mapping[str, Sequence[Allele]]):

src/automlst/engine/remote/databases/institutpasteur/mlst.py

@@ -3,7 +3,7 @@ from contextlib import AbstractAsyncContextManager
 import re
 from typing import Any, AsyncGenerator, AsyncIterable, Generator, Iterable, Sequence, Union
 from aiohttp import ClientSession, ClientTimeout
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 from automlst.engine.data.genomics import NamedString
 
 class InstitutPasteurProfiler(AbstractAsyncContextManager):

src/automlst/engine/remote/databases/mlst.py

@@ -4,7 +4,7 @@ from typing import AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping,
 
 from aiohttp import ClientSession
 
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 
 MLST_DATABASES = [
     "https://bigsdb.pasteur.fr/api/db",

src/automlst/engine/remote/databases/pubmlst/mlst.py

@@ -3,7 +3,7 @@ from contextlib import AbstractAsyncContextManager
 import re
 from typing import Any, AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping, Sequence, Union
 from aiohttp import ClientSession, ClientTimeout
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 from automlst.engine.data.genomics import NamedString
 from automlst.engine.remote.databases.mlst import MLSTProfiler
 

tests/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/test_mlst.py

@@ -1,5 +1,5 @@
 from Bio import SeqIO
-from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.data.mlst import Allele, MLSTProfile
 from automlst.engine.remote.databases.institutpasteur.mlst import InstitutPasteurProfiler
 
 
@@ -32,4 +32,22 @@ async def test_profiling_results_in_correct_st():
         assert mlst_st_data is not None
         assert isinstance(mlst_st_data, MLSTProfile)
         assert mlst_st_data.clonal_complex == "ST-2 complex"
-        assert mlst_st_data.sequence_type == "1"
+        assert mlst_st_data.sequence_type == "1"
+
+async def test_sequence_profiling_is_correct():
+    sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
+    dummy_alleles = [
+        Allele("adk", "1"),
+        Allele("fumC", "1"),
+        Allele("glyA", "1"),
+        Allele("tyrB", "1"),
+        Allele("icd", "1"),
+        Allele("pepA", "1"),
+        Allele("pgm", "1"),
+    ]
+    async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
+        profile = await dummy_profiler.profile_string(sequence)
+        assert profile is not None
+        assert isinstance(profile, MLSTProfile)
+        assert profile.clonal_complex == "ST-2 complex"
+        assert profile.sequence_type == "1"