Merge branch 'features/improved-oop-architecture' into features/non-exact-notation

src/autobigs/engine/analysis/aligners.py

@@ -1,70 +0,0 @@
-import asyncio
-from concurrent.futures import Future, ThreadPoolExecutor
-from contextlib import AbstractContextManager
-from typing import Any, Set, Union
-from Bio.Align import PairwiseAligner
-from queue import Queue
-
-from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignment
-
-class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager):
-    def __enter__(self):
-        self._thread_pool = ThreadPoolExecutor(self._max_threads, thread_name_prefix="async-pairwise-alignment")
-        return self
-
-    def __init__(self, aligner: PairwiseAligner, max_threads: int = 4):
-        self._max_threads = max_threads
-        self._aligner = aligner
-        self._work_left: Set[Future] = set()
-        self._work_complete: Queue[Future] = Queue()
-
-    def align(self, reference: str, query: str, **associated_data):
-        work = self._thread_pool.submit(
-            self.work, reference, query, **associated_data)
-        work.add_done_callback(self._on_complete)
-        self._work_left.add(work)
-        
-    def _on_complete(self, future: Future):
-        self._work_left.remove(future)
-        self._work_complete.put(future)
-
-    def work(self, reference, query, **associated_data):
-        alignments = self._aligner.align(reference, query)
-        top_alignment = alignments[0]
-        top_alignment_stats = top_alignment.counts()
-        top_alignment_gaps = top_alignment_stats.gaps
-        top_alignment_identities = top_alignment_stats.identities
-        top_alignment_mismatches = top_alignment_stats.mismatches
-        top_alignment_score = top_alignment.score # type: ignore
-        return PairwiseAlignment(
-            top_alignment.sequences[0],
-            top_alignment.sequences[1],
-            tuple(top_alignment.indices[0]),
-            tuple(top_alignment.indices[1]),
-            AlignmentStats(
-                percent_identity=top_alignment_identities/top_alignment.length,
-                mismatches=top_alignment_mismatches,
-                gaps=top_alignment_gaps,
-                match_metric=top_alignment_score
-            )), associated_data
-
-    async def next_completed(self) -> Union[tuple[PairwiseAlignment, dict[str, Any]], None]:
-        if self._work_complete.empty() and len(self._work_left):
-            return None
-        completed_alignment = await asyncio.wrap_future(self._work_complete.get())
-        return completed_alignment
-
-    def __exit__(self, exc_type, exc_value, traceback):
-        self.shutdown()
-
-    def __aiter__(self):
-        return self
-    
-    async def __anext__(self):
-        result = await self.next_completed()
-        if result is None:
-            raise StopAsyncIteration
-        return result
-
-    def shutdown(self):
-        self._thread_pool.shutdown(wait=True, cancel_futures=True)

src/autobigs/engine/analysis/genbank.py

@@ -1,26 +0,0 @@
-import asyncio
-from contextlib import AbstractAsyncContextManager
-import tempfile
-from typing import Iterable, Union
-from Bio import Entrez
-from Bio import SeqIO
-
-from autobigs.engine.structures.genomics import AnnotatedString, StringAnnotation
-
-async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:
-    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)
-            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=qualifiers
-            ))
-        return AnnotatedString(name=genbank_id, sequence=str(record.seq), annotations=sequence_features)

tests/autobigs/engine/analysis/test_aligners.py

@@ -1,42 +0,0 @@
-from Bio import SeqIO
-from Bio.Align import PairwiseAligner
-from pytest import mark
-from pytest import fixture
-from autobigs.engine.analysis.aligners import AsyncBiopythonPairwiseAlignmentEngine
-from autobigs.engine.structures.alignment import PairwiseAlignment
-
-@fixture
-def tohamaI_bpertussis_adk():
-    return str(SeqIO.read("tests/resources/tohama_I_bpertussis_adk.fasta", format="fasta").seq)
-
-@fixture
-def tohamaI_bpertussis_genome():
-    return str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", format="fasta").seq)
-
-@fixture
-def fdaargos_1560_hinfluenza_adk():
-    return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza_adk.fasta", format="fasta").seq)
-
-@fixture
-def fdaargos_1560_hinfluenza_genome():
-    return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza.fasta", format="fasta").seq)
-
-
-@fixture(params=[1, 2])
-def dummy_engine(request):
-    aligner = PairwiseAligner("blastn")
-    aligner.mode = "local"
-    with AsyncBiopythonPairwiseAlignmentEngine(aligner, request.param) as engine:
-        yield engine
-
-class TestAsyncPairwiseAlignmentEngine:
-    async def test_single_alignment_no_errors_single_alignment(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
-        dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
-        async for alignment, additional_information in dummy_engine:
-            assert isinstance(alignment, PairwiseAlignment)
-
-    async def test_single_alignment_no_errors_multiple(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk, fdaargos_1560_hinfluenza_genome, fdaargos_1560_hinfluenza_adk, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
-        dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
-        dummy_engine.align(fdaargos_1560_hinfluenza_genome, fdaargos_1560_hinfluenza_adk)
-        async for alignment, additional_information in dummy_engine:
-            assert isinstance(alignment, PairwiseAlignment)

tests/autobigs/engine/analysis/test_bigsdb.py

@@ -61,12 +61,12 @@ hinfluenzae_fdaargos_profile = MLSTProfile((
     ), "3", "ST-3 complex")
 
 hinfluenzae_fdaargos_bad_profile = MLSTProfile((
-        Allele("adk", "1", None),
+        Allele("adk", "3", None),
-        Allele("atpG", "1", None),
+        Allele("atpG", "121", None),
-        Allele("frdB", "1", None),
+        Allele("frdB", "6", None),
-        Allele("fucK", "1", None),
+        Allele("fucK", "5", None),
-        Allele("mdh", "1", None),
+        Allele("mdh", "12", None),
-        Allele("pgi", "1", None),
+        Allele("pgi", "4", None),
         Allele("recA", "5", None)
     ), "3", "ST-3 complex")
 
@@ -76,7 +76,7 @@ hinfluenzae_fdaargos_fragmented_sequence = tuple(SeqIO.parse("tests/resources/to
 
 @pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [
     (False, "https://bigsdb.pasteur.fr/api", "pubmlst_bordetella_seqdef", 3, "tohama_I_bpertussis.fasta", "tohama_I_bpertussis_features.fasta", bpertussis_tohamaI_profile, bpertussis_tohamaI_bad_profile),
-    (False, "https://bigsdb.pasteur.fr/api", "pubmlst_hinfluenzae_seqdef", 1, "fdaargos_1560_hinfluenza.fasta", "fdaargos_1560_hinfluenza_features.fasta", hinfluenzae_fdaargos_profile, hinfluenzae_fdaargos_bad_profile),
+    (False, "https://rest.pubmlst.org", "pubmlst_hinfluenzae_seqdef", 1, "fdaargos_1560_hinfluenza.fasta", "fdaargos_1560_hinfluenza_features.fasta", hinfluenzae_fdaargos_profile, hinfluenzae_fdaargos_bad_profile),
 ])
 class TestBIGSdbMLSTProfiler:
     async def test_profiling_results_in_exact_matches_when_exact(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):