Completed NCBI lookup, FASTA reading, ABIF reading, and Institut Pasteur querying

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

@@ -0,0 +1,16 @@
+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/ncbi/test_genbank.py

@@ -0,0 +1,5 @@
+from mlstmyfasta.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