Wrote simple annotation test

src/mlstmyfasta/engine/annotations.py

@@ -1,34 +1,42 @@
+import asyncio
 from typing import Any, Generator, List, Sequence
 from Bio.Align import PairwiseAligner
 from Bio import Entrez
 from Bio import SeqIO
+import numpy as np
 
-from mlstmyfasta.engine.data.genomics import Strand, StrandFeature, get_feature_coding
+from mlstmyfasta.engine.data.genomics import AnnotatedString, StringAnnotation, get_feature_coding
 
 
-async def fetch_ncbi_genbank(genbank_id: str) -> Strand:
+async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:
-    with Entrez.efetch(db="nucleotide", id=genbank_id, rettype="gb", retmode="text") as fetch_stream:
+    with (await asyncio.to_thread(Entrez.efetch, db="nucleotide", id=genbank_id, rettype="gb", retmode="text")) as fetch_stream:
         record = SeqIO.read(fetch_stream, "genbank")
         sequence_features = list()
         for feature in record.features:
             start = int(feature.location.start)
             end = int(feature.location.end)
-            sequence_features.append(StrandFeature(
+            sequence_features.append(StringAnnotation(
                 type=feature.type,
                 start=start,
                 end=end+1,  # Position is exclusive
                 feature_properties=feature.qualifiers
             ))
-        return Strand(name=genbank_id, coding=str(record.seq), features=sequence_features)
+        return AnnotatedString(name=genbank_id, sequence=str(record.seq), annotations=sequence_features)
 
 
-async def annotate_from_genbank(genbank_id: str, query_coding: str):
+async def annotate_from_genbank(genbank_id: str, query_coding: str, max_annotation_length=1000):
-    strand = await fetch_ncbi_genbank(genbank_id=genbank_id)
+    reference_annotations = await fetch_ncbi_genbank(genbank_id=genbank_id)
     aligner = PairwiseAligner("blastn")
     aligner.mode = "local"
-    for feature in strand.features:
+    for annotation in reference_annotations.annotations:
-        feature_coding = get_feature_coding(strand=strand, feature=feature)
+        if annotation.end - annotation.start > max_annotation_length:
-        if len(aligner.align(query_coding, feature)) < 1:
             # TODO implement a failsafe
             continue
-        sequence = sorted(aligner.align(query_coding, feature))[0]
+        feature_string_sequence = get_feature_coding(annotated_string=reference_annotations, string_annotation=annotation)
+        alignments = aligner.align(query_coding, feature_string_sequence)
+        if len(alignments) < 1:
+            # TODO implement a failsafe
+            continue
+        top_alignment = sorted(aligner.align(query_coding, annotation))[0]
+        # TODO Check if alternatives are better
+        

src/mlstmyfasta/engine/data/genomics.py

@@ -3,17 +3,17 @@ from typing import Mapping, Sequence
 
 
 @dataclass
-class StrandFeature:
+class StringAnnotation:
     type: str
     start: int
     end: int
     feature_properties: Mapping[str, Sequence[str]]
     
 @dataclass
-class Strand:
+class AnnotatedString:
     name: str
-    coding: str
+    sequence: str
-    features: Sequence[StrandFeature]
+    annotations: Sequence[StringAnnotation]
 
-def get_feature_coding(strand: Strand, feature: StrandFeature) -> str:
+def get_feature_coding(annotated_string: AnnotatedString, string_annotation: StringAnnotation) -> str:
-    return strand.coding[feature.start:feature.end]
+    return annotated_string.sequence[string_annotation.start:string_annotation.end]

tests/mlstmyfasta/engine/test_annotations.py

@@ -1,6 +1,11 @@
-from mlstmyfasta.engine.annotations import fetch_ncbi_genbank
+from mlstmyfasta.engine.annotations import annotate_from_genbank, fetch_ncbi_genbank
+from Bio import SeqIO
 
+from mlstmyfasta.engine.data.genomics import AnnotatedString
 
 async def test_fetch_ncbi_genbank_with_id_works():
-    assert len((await fetch_ncbi_genbank("CP011448.1")).coding) > 0 
+    assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0 
-    
+
+async def test_annotate_from_genbank_results_in_annotations():
+    sequence = SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq
+    assert (await annotate_from_genbank("CP011448.1", str(sequence))) is AnnotatedString