Merge branch 'features/improved-oop-architecture' into features/non-exact-notation
This commit is contained in:
commit
36bca1b70d
@ -1,70 +0,0 @@
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import asyncio
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from concurrent.futures import Future, ThreadPoolExecutor
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from contextlib import AbstractContextManager
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from typing import Any, Set, Union
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from Bio.Align import PairwiseAligner
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from queue import Queue
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from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignment
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class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager):
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def __enter__(self):
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self._thread_pool = ThreadPoolExecutor(self._max_threads, thread_name_prefix="async-pairwise-alignment")
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return self
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def __init__(self, aligner: PairwiseAligner, max_threads: int = 4):
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self._max_threads = max_threads
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self._aligner = aligner
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self._work_left: Set[Future] = set()
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self._work_complete: Queue[Future] = Queue()
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def align(self, reference: str, query: str, **associated_data):
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work = self._thread_pool.submit(
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self.work, reference, query, **associated_data)
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work.add_done_callback(self._on_complete)
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self._work_left.add(work)
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def _on_complete(self, future: Future):
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self._work_left.remove(future)
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self._work_complete.put(future)
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def work(self, reference, query, **associated_data):
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alignments = self._aligner.align(reference, query)
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top_alignment = alignments[0]
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top_alignment_stats = top_alignment.counts()
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top_alignment_gaps = top_alignment_stats.gaps
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top_alignment_identities = top_alignment_stats.identities
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top_alignment_mismatches = top_alignment_stats.mismatches
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top_alignment_score = top_alignment.score # type: ignore
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return PairwiseAlignment(
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top_alignment.sequences[0],
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top_alignment.sequences[1],
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tuple(top_alignment.indices[0]),
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tuple(top_alignment.indices[1]),
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AlignmentStats(
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percent_identity=top_alignment_identities/top_alignment.length,
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mismatches=top_alignment_mismatches,
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gaps=top_alignment_gaps,
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match_metric=top_alignment_score
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)), associated_data
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async def next_completed(self) -> Union[tuple[PairwiseAlignment, dict[str, Any]], None]:
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if self._work_complete.empty() and len(self._work_left):
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return None
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completed_alignment = await asyncio.wrap_future(self._work_complete.get())
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return completed_alignment
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def __exit__(self, exc_type, exc_value, traceback):
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self.shutdown()
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def __aiter__(self):
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return self
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async def __anext__(self):
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result = await self.next_completed()
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if result is None:
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raise StopAsyncIteration
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return result
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def shutdown(self):
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self._thread_pool.shutdown(wait=True, cancel_futures=True)
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@ -1,26 +0,0 @@
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import asyncio
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from contextlib import AbstractAsyncContextManager
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import tempfile
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from typing import Iterable, Union
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from Bio import Entrez
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from Bio import SeqIO
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from autobigs.engine.structures.genomics import AnnotatedString, StringAnnotation
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async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:
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with (await asyncio.to_thread(Entrez.efetch, db="nucleotide", id=genbank_id, rettype="gb", retmode="text")) as fetch_stream:
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record = SeqIO.read(fetch_stream, "genbank")
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sequence_features = list()
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for feature in record.features:
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start = int(feature.location.start)
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end = int(feature.location.end)
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qualifiers = feature.qualifiers
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for qualifier_key in qualifiers:
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qualifiers[qualifier_key] = set(qualifiers[qualifier_key])
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sequence_features.append(StringAnnotation(
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type=feature.type,
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start=start,
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end=end+1, # Position is exclusive
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feature_properties=qualifiers
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))
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return AnnotatedString(name=genbank_id, sequence=str(record.seq), annotations=sequence_features)
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@ -1,42 +0,0 @@
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from Bio import SeqIO
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from Bio.Align import PairwiseAligner
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from pytest import mark
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from pytest import fixture
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from autobigs.engine.analysis.aligners import AsyncBiopythonPairwiseAlignmentEngine
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from autobigs.engine.structures.alignment import PairwiseAlignment
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@fixture
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def tohamaI_bpertussis_adk():
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return str(SeqIO.read("tests/resources/tohama_I_bpertussis_adk.fasta", format="fasta").seq)
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@fixture
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def tohamaI_bpertussis_genome():
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return str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", format="fasta").seq)
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@fixture
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def fdaargos_1560_hinfluenza_adk():
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return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza_adk.fasta", format="fasta").seq)
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@fixture
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def fdaargos_1560_hinfluenza_genome():
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return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza.fasta", format="fasta").seq)
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@fixture(params=[1, 2])
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def dummy_engine(request):
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aligner = PairwiseAligner("blastn")
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aligner.mode = "local"
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with AsyncBiopythonPairwiseAlignmentEngine(aligner, request.param) as engine:
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yield engine
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class TestAsyncPairwiseAlignmentEngine:
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async def test_single_alignment_no_errors_single_alignment(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
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dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
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async for alignment, additional_information in dummy_engine:
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assert isinstance(alignment, PairwiseAlignment)
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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):
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dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
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dummy_engine.align(fdaargos_1560_hinfluenza_genome, fdaargos_1560_hinfluenza_adk)
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async for alignment, additional_information in dummy_engine:
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assert isinstance(alignment, PairwiseAlignment)
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@ -61,12 +61,12 @@ hinfluenzae_fdaargos_profile = MLSTProfile((
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), "3", "ST-3 complex")
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hinfluenzae_fdaargos_bad_profile = MLSTProfile((
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Allele("adk", "1", None),
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Allele("atpG", "1", None),
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Allele("frdB", "1", None),
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Allele("fucK", "1", None),
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Allele("mdh", "1", None),
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Allele("pgi", "1", None),
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Allele("adk", "3", None),
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Allele("atpG", "121", None),
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Allele("frdB", "6", None),
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Allele("fucK", "5", None),
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Allele("mdh", "12", None),
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Allele("pgi", "4", None),
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Allele("recA", "5", None)
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), "3", "ST-3 complex")
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@ -76,7 +76,7 @@ hinfluenzae_fdaargos_fragmented_sequence = tuple(SeqIO.parse("tests/resources/to
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@pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [
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(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),
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(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),
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(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),
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])
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class TestBIGSdbMLSTProfiler:
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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):
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