Completed CLI for B. pertussis MLST typing from fasta files

tests/mlstmyfasta/engine/local/test_abif.py

@@ -1,8 +1,8 @@
 import os
 
-from mlstmyfasta.engine.local.abif import load_sanger_sequence
+from mlstmyfasta.engine.local.abif import read_abif
 
 async def test_load_sanger_sequence_has_data():
     assert os.path.exists("tests/resources/1I1_F_P1815443_047.ab1")
-    result_data = await load_sanger_sequence("tests/resources/1I1_F_P1815443_047.ab1")
+    result_data = await read_abif("tests/resources/1I1_F_P1815443_047.ab1")
     assert result_data is not None

tests/mlstmyfasta/engine/remote/databases/institutpasteur/test_profiles.py

@@ -1,16 +0,0 @@
-from Bio import SeqIO
-from mlstmyfasta.engine.data.MLST import Allele
-from mlstmyfasta.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_profile(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

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

@@ -0,0 +1,35 @@
+from Bio import SeqIO
+from mlstmyfasta.engine.data.MLST import Allele, MLSTProfile
+from mlstmyfasta.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"