Copied over most code from another of my projects

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

@@ -0,0 +1,35 @@
+from Bio import SeqIO
+from automlst.engine.data.MLST import Allele, MLSTProfile
+from automlst.engine.remote.databases.institutpasteur.profiling import InstitutPasteurProfiler
+
+
+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)
+        targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
+        async for exact_match in exact_matches:
+            assert isinstance(exact_match, Allele)
+            assert exact_match.allele_variant == '1' # All of Tohama I has allele id I
+            targets_left.remove(exact_match.allele_loci)
+
+        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"),
+        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:
+        exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
+        mlst_st_data = await dummy_profiler.fetch_mlst_st(dummy_alleles)
+        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"

tests/nsbdiagnosistoolkit/engine/remote/databases/ncbi/test_genbank.py

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+from automlst.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
+
+
+async def test_fetch_ncbi_genbank_with_id_works():
+    assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0