Tested annotation alignment system

.devcontainer/devcontainer.json

@@ -12,8 +12,7 @@
 			"extensions": [
 				"ms-python.isort",
 				"njpwerner.autodocstring",
-				"ms-python.black-formatter",
-				"ms-python.pylint"
+				"ms-python.black-formatter"
 			]
 		}
 	},

requirements.txt

@@ -1,4 +1,4 @@
-requests
+aiohttp[speedups]
 biopython
 pytest
 pytest-asyncio

src/mlstmyfasta/engine/annotations.py

@@ -1,10 +1,15 @@
 import asyncio
+from collections.abc import Set
 from typing import Any, Generator, List, Sequence
 from Bio.Align import PairwiseAligner
 from Bio import Entrez
 from Bio import SeqIO
 import numpy as np
 
+
+# TODO Change this out for a more professional approach
+Entrez.email = "yunyangdeng@outlook.com"
+
 from mlstmyfasta.engine.data.genomics import AnnotatedString, StringAnnotation, get_feature_coding
 
 
@@ -15,22 +20,31 @@ async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:
         for feature in record.features:
             start = int(feature.location.start)
             end = int(feature.location.end)
+            qualifiers = feature.qualifiers
+            for qualifier_key in qualifiers:
+                qualifiers[qualifier_key] = set(qualifiers[qualifier_key])
             sequence_features.append(StringAnnotation(
                 type=feature.type,
                 start=start,
                 end=end+1,  # Position is exclusive
-                feature_properties=feature.qualifiers
+                feature_properties=qualifiers
             ))
         return AnnotatedString(name=genbank_id, sequence=str(record.seq), annotations=sequence_features)
 
 
-async def annotate_from_genbank(genbank_id: str, query_name: str, query_string: str, max_annotation_length=750):
+async def annotate_from_genbank(genbank_id: str, query_name: str, query_string: str, max_annotation_length:int = 512, gene_targets:Set = set()):
+    # TODO implement asynchronous alignment algorithm
     reference_annotations = await fetch_ncbi_genbank(genbank_id=genbank_id)
     query_annotations = list()
     aligner = PairwiseAligner("blastn")
     aligner.mode = "local"
     for annotation in reference_annotations.annotations:
-        if annotation.end - annotation.start > max_annotation_length:
+        if annotation.type != "gene" or "gene" not in annotation.feature_properties:
+            continue
+        if len(gene_targets) > 0 and "gene" in annotation.feature_properties:
+            if not annotation.feature_properties["gene"].intersection(gene_targets):
+                continue
+        if max_annotation_length > 0 and annotation.end - annotation.start > max_annotation_length:
             # TODO implement a failsafe
             continue
         feature_string_sequence = get_feature_coding(annotated_string=reference_annotations, string_annotation=annotation)
@@ -38,7 +52,7 @@ async def annotate_from_genbank(genbank_id: str, query_name: str, query_string:
         if len(alignments) < 1:
             # TODO implement a failsafe
             continue
-        top_alignment = sorted(aligner.align(query_string, annotation))[0]
+        top_alignment = sorted(alignments)[0]
         # TODO Check if alternatives are better
         query_annotations.append(StringAnnotation(
             type=annotation.type, # same as original

src/mlstmyfasta/engine/data/genomics.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass
-from typing import Mapping, Sequence
+from typing import Mapping, Sequence, Set
 
 
 @dataclass
@@ -7,7 +7,7 @@ class StringAnnotation:
     type: str
     start: int
     end: int
-    feature_properties: Mapping[str, Sequence[str]]
+    feature_properties: Mapping[str, Set[str]]
     
 @dataclass
 class AnnotatedString:

src/mlstmyfasta/engine/external/databases/institutpasteur/query.py

@@ -1,13 +0,0 @@
-import json
-import requests
-from mlstmyfasta.engine.data import MLST
-from mlstmyfasta.engine.external.databases.institutpasteur.structures import SequenceRequestBody
-from mlstmyfasta.engine.external.databases.institutpasteur.structures import SequenceResponse
-
-async def query_fasta_mlst_profile(database: str, request_body: SequenceRequestBody):
-    url: str = f"https://bigsdb.pasteur.fr/api/db/{database}/mlst/sequence"
-    request_result = requests.post(url, json=json.dumps(request_body), timeout=10000)
-    seq_result: SequenceResponse = request_result.json()
-    result = list()
-    for exact_match in seq_result.exact_matches:
-        result.append(MLST.Allele())

tests/mlstmyfasta/engine/test_annotations.py

@@ -6,7 +6,10 @@ from mlstmyfasta.engine.data.genomics import AnnotatedString
 async def test_fetch_ncbi_genbank_with_id_works():
     assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0 
 
-async def test_annotate_from_genbank_results_in_annotations():
+async def test_annotate_from_genbank_for_adk_annotation():
     sequence = SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq
-    annotated_sequence = await annotate_from_genbank("CP011448.1", "bpertussis_tohamaI", str(sequence))
-    assert annotated_sequence is AnnotatedString
+    annotated_sequence = await annotate_from_genbank("CP011448.1", "bpertussis_tohamaI", str(sequence), max_annotation_length=750, gene_targets=set(["adk"]))
+    assert isinstance(annotated_sequence, AnnotatedString)
+    assert len(annotated_sequence.annotations) >= 1
+    assert annotated_sequence.annotations[0].type == "gene"
+    assert "adk" in annotated_sequence.annotations[0].feature_properties["gene"]