began adding PubMLST support

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

@@ -6,7 +6,7 @@ from automlst.engine.remote.databases.institutpasteur.mlst import InstitutPasteu
 async def test_profiling_results_in_exact_matches_when_exact():
     sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
     async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
-        exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
+        exact_matches = dummy_profiler.fetch_mlst_allele_variants(schema_id=3, sequence_string=sequence)
         targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
         async for exact_match in exact_matches:
             assert isinstance(exact_match, Allele)
@@ -16,7 +16,6 @@ async def test_profiling_results_in_exact_matches_when_exact():
         assert len(targets_left) == 0
 
 async def test_profiling_results_in_correct_st():
-    sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
     dummy_alleles = [
         Allele("adk", "1"),
         Allele("fumC", "1"),
@@ -27,8 +26,7 @@ async def test_profiling_results_in_correct_st():
         Allele("pgm", "1"),
     ]
     async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
-        exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
-        mlst_st_data = await dummy_profiler.fetch_mlst_st(dummy_alleles)
+        mlst_st_data = await dummy_profiler.fetch_mlst_st(3, dummy_alleles)
         assert mlst_st_data is not None
         assert isinstance(mlst_st_data, MLSTProfile)
         assert mlst_st_data.clonal_complex == "ST-2 complex"
@@ -46,7 +44,7 @@ async def test_sequence_profiling_is_correct():
         Allele("pgm", "1"),
     ]
     async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
-        profile = await dummy_profiler.profile_string(sequence)
+        profile = await dummy_profiler.profile_string(3, sequence)
         assert profile is not None
         assert isinstance(profile, MLSTProfile)
         assert profile.clonal_complex == "ST-2 complex"

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

@@ -0,0 +1,50 @@
+from Bio import SeqIO
+from automlst.engine.data.mlst import Allele, MLSTProfile
+from automlst.engine.remote.databases.institutpasteur.mlst import InstitutPasteurProfiler
+from automlst.engine.remote.databases.pubmlst.mlst import PubMLSTProfiler
+
+
+async def test_profiling_results_in_exact_matches_when_exact():
+    dummy_alleles = {
+        Allele("adk", "1"),
+        Allele("atpG", "1"),
+        Allele("frdB", "1"),
+        Allele("fucK", "1"),
+        Allele("mdh", "1"),
+        Allele("pgi", "1"),
+        Allele("recA", "5"),
+    }
+    sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
+    async with PubMLSTProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
+        exact_matches = dummy_profiler.fetch_mlst_allele_variants(schema_id=1, sequence_string=sequence)
+        async for exact_match in exact_matches:
+            assert isinstance(exact_match, Allele)
+            dummy_alleles.remove(exact_match)
+
+        assert len(dummy_alleles) == 0
+
+async def test_profiling_results_in_correct_st():
+    dummy_alleles = [
+        Allele("adk", "1"),
+        Allele("atpG", "1"),
+        Allele("frdB", "1"),
+        Allele("fucK", "1"),
+        Allele("mdh", "1"),
+        Allele("pgi", "1"),
+        Allele("recA", "5"),
+    ]
+    async with InstitutPasteurProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
+        mlst_st_data = await dummy_profiler.fetch_mlst_st(1, dummy_alleles)
+        assert mlst_st_data is not None
+        assert isinstance(mlst_st_data, MLSTProfile)
+        assert mlst_st_data.clonal_complex == "ST-3 complex"
+        assert mlst_st_data.sequence_type == "3"
+
+async def test_sequence_profiling_is_correct():
+    sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
+    async with InstitutPasteurProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
+        profile = await dummy_profiler.profile_string(1, sequence)
+        assert profile is not None
+        assert isinstance(profile, MLSTProfile)
+        assert profile.clonal_complex == "ST-3 complex"
+        assert profile.sequence_type == "3"