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Added unit tests for pubMLST MLST profiling

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This commit is contained in:
Harrison Deng
2025-01-08 17:34:30 +00:00
parent 424beeb559
commit 645357ac58
5 changed files with 110 additions and 105 deletions
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163
src/automlst/engine/local/abif.py
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@@ -1,7 +1,7 @@
import asyncio
from numbers import Number
from os import path
from typing import AsyncGenerator, Collection, Sequence, Union
from typing import Any, AsyncGenerator, Collection, Sequence, Union
from automlst.engine.data.genomics import NamedString, SangerTraceData
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO, Align
@@ -21,95 +21,98 @@ async def read_abif(seq_path: str) -> SangerTraceData:
biopython_annotations = biopython_seq.annotations
# Lot of type ignoring since Biopython did not define their typing.
biopython_abif_raw = biopython_annotations["abif_raw"] # type: ignore
biopython_abif_raw = biopython_annotations["abif_raw"] # type: ignore
trace_data = SangerTraceData(
path.basename(seq_path),
biopython_seq.seq,
biopython_abif_raw.get("APFN2"), # type: ignore
biopython_abif_raw.get("APrN1"), # type: ignore
biopython_abif_raw.get("APrV1"), # type: ignore
biopython_abif_raw.get("APrX1"), # type: ignore
biopython_abif_raw.get("APXV1"), # type: ignore
biopython_abif_raw.get("CMNT1"), # type: ignore
biopython_abif_raw.get("CpEP1"), # type: ignore
biopython_abif_raw.get("CTID1"), # type: ignore
biopython_abif_raw.get("CTNM1"), # type: ignore
biopython_abif_raw.get("CTTL1"), # type: ignore
biopython_abif_raw.get("DATA1"), # type: ignore
biopython_abif_raw.get("DATA2"), # type: ignore
biopython_abif_raw.get("DATA3"), # type: ignore
biopython_abif_raw.get("DATA4"), # type: ignore
biopython_abif_raw.get("DATA5"), # type: ignore
biopython_abif_raw.get("DATA6"), # type: ignore
biopython_abif_raw.get("DATA7"), # type: ignore
biopython_abif_raw.get("DATA8"), # type: ignore
biopython_abif_raw.get("DSam1"), # type: ignore
biopython_abif_raw.get("DyeN1"), # type: ignore
biopython_abif_raw.get("DyeN2"), # type: ignore
biopython_abif_raw.get("DyeN3"), # type: ignore
biopython_abif_raw.get("DyeN4"), # type: ignore
biopython_abif_raw.get("DyeW1"), # type: ignore
biopython_abif_raw.get("DyeW2"), # type: ignore
biopython_abif_raw.get("DyeW3"), # type: ignore
biopython_abif_raw.get("DyeW4"), # type: ignore
biopython_abif_raw.get("DySN1"), # type: ignore
biopython_abif_raw.get("EPVt1"), # type: ignore
biopython_abif_raw.get("EVNT1"), # type: ignore
biopython_abif_raw.get("EVNT2"), # type: ignore
biopython_abif_raw.get("EVNT3"), # type: ignore
biopython_abif_raw.get("EVNT4"), # type: ignore
biopython_abif_raw.get("FWO_1"), # type: ignore
biopython_abif_raw.get("GTyp1"), # type: ignore
biopython_abif_raw.get("InSc1"), # type: ignore
biopython_abif_raw.get("InVt1"), # type: ignore
biopython_abif_raw.get("LANE1"), # type: ignore
biopython_abif_raw.get("LIMS1"), # type: ignore
biopython_abif_raw.get("LNTD1"), # type: ignore
biopython_abif_raw.get("LsrP1"), # type: ignore
biopython_abif_raw.get("MCHN1"), # type: ignore
biopython_abif_raw.get("MODF1"), # type: ignore
biopython_abif_raw.get("MODL1"), # type: ignore
biopython_abif_raw.get("NAVG1"), # type: ignore
biopython_abif_raw.get("NLNE1"), # type: ignore
biopython_abif_raw.get("OfSc1"), # type: ignore
biopython_abif_raw.get("PDMF1"), # type: ignore
biopython_abif_raw.get("PXLB1"), # type: ignore
biopython_abif_raw.get("RGCm1"), # type: ignore
biopython_abif_raw.get("RGNm1"), # type: ignore
biopython_abif_raw.get("RMdV1"), # type: ignore
biopython_abif_raw.get("RMdX1"), # type: ignore
biopython_abif_raw.get("RMXV1"), # type: ignore
biopython_abif_raw.get("RPrN1"), # type: ignore
biopython_abif_raw.get("RPrV1"), # type: ignore
biopython_abif_raw.get("RUND1"), # type: ignore
biopython_abif_raw.get("RUND2"), # type: ignore
biopython_abif_raw.get("RUND3"), # type: ignore
biopython_abif_raw.get("RUND4"), # type: ignore
biopython_abif_raw.get("RunN1"), # type: ignore
biopython_abif_raw.get("RUNT1"), # type: ignore
biopython_abif_raw.get("RUNT2"), # type: ignore
biopython_abif_raw.get("RUNT3"), # type: ignore
biopython_abif_raw.get("RUNT4"), # type: ignore
biopython_abif_raw.get("Satd"), # type: ignore
biopython_abif_raw.get("Scal1"), # type: ignore
biopython_abif_raw.get("SCAN1"), # type: ignore
biopython_abif_raw.get("SMED1"), # type: ignore
biopython_abif_raw.get("SMLt"), # type: ignore
biopython_abif_raw.get("SMPL1"), # type: ignore
biopython_abif_raw.get("SVER1"), # type: ignore
biopython_abif_raw.get("SVER3"), # type: ignore
biopython_abif_raw.get("Tmpr1"), # type: ignore
biopython_abif_raw.get("TUBE"), # type: ignore
biopython_abif_raw.get("User") # type: ignore
biopython_abif_raw.get("APFN2"), # type: ignore
biopython_abif_raw.get("APrN1"), # type: ignore
biopython_abif_raw.get("APrV1"), # type: ignore
biopython_abif_raw.get("APrX1"), # type: ignore
biopython_abif_raw.get("APXV1"), # type: ignore
biopython_abif_raw.get("CMNT1"), # type: ignore
biopython_abif_raw.get("CpEP1"), # type: ignore
biopython_abif_raw.get("CTID1"), # type: ignore
biopython_abif_raw.get("CTNM1"), # type: ignore
biopython_abif_raw.get("CTTL1"), # type: ignore
biopython_abif_raw.get("DATA1"), # type: ignore
biopython_abif_raw.get("DATA2"), # type: ignore
biopython_abif_raw.get("DATA3"), # type: ignore
biopython_abif_raw.get("DATA4"), # type: ignore
biopython_abif_raw.get("DATA5"), # type: ignore
biopython_abif_raw.get("DATA6"), # type: ignore
biopython_abif_raw.get("DATA7"), # type: ignore
biopython_abif_raw.get("DATA8"), # type: ignore
biopython_abif_raw.get("DSam1"), # type: ignore
biopython_abif_raw.get("DyeN1"), # type: ignore
biopython_abif_raw.get("DyeN2"), # type: ignore
biopython_abif_raw.get("DyeN3"), # type: ignore
biopython_abif_raw.get("DyeN4"), # type: ignore
biopython_abif_raw.get("DyeW1"), # type: ignore
biopython_abif_raw.get("DyeW2"), # type: ignore
biopython_abif_raw.get("DyeW3"), # type: ignore
biopython_abif_raw.get("DyeW4"), # type: ignore
biopython_abif_raw.get("DySN1"), # type: ignore
biopython_abif_raw.get("EPVt1"), # type: ignore
biopython_abif_raw.get("EVNT1"), # type: ignore
biopython_abif_raw.get("EVNT2"), # type: ignore
biopython_abif_raw.get("EVNT3"), # type: ignore
biopython_abif_raw.get("EVNT4"), # type: ignore
biopython_abif_raw.get("FWO_1"), # type: ignore
biopython_abif_raw.get("GTyp1"), # type: ignore
biopython_abif_raw.get("InSc1"), # type: ignore
biopython_abif_raw.get("InVt1"), # type: ignore
biopython_abif_raw.get("LANE1"), # type: ignore
biopython_abif_raw.get("LIMS1"), # type: ignore
biopython_abif_raw.get("LNTD1"), # type: ignore
biopython_abif_raw.get("LsrP1"), # type: ignore
biopython_abif_raw.get("MCHN1"), # type: ignore
biopython_abif_raw.get("MODF1"), # type: ignore
biopython_abif_raw.get("MODL1"), # type: ignore
biopython_abif_raw.get("NAVG1"), # type: ignore
biopython_abif_raw.get("NLNE1"), # type: ignore
biopython_abif_raw.get("OfSc1"), # type: ignore
biopython_abif_raw.get("PDMF1"), # type: ignore
biopython_abif_raw.get("PXLB1"), # type: ignore
biopython_abif_raw.get("RGCm1"), # type: ignore
biopython_abif_raw.get("RGNm1"), # type: ignore
biopython_abif_raw.get("RMdV1"), # type: ignore
biopython_abif_raw.get("RMdX1"), # type: ignore
biopython_abif_raw.get("RMXV1"), # type: ignore
biopython_abif_raw.get("RPrN1"), # type: ignore
biopython_abif_raw.get("RPrV1"), # type: ignore
biopython_abif_raw.get("RUND1"), # type: ignore
biopython_abif_raw.get("RUND2"), # type: ignore
biopython_abif_raw.get("RUND3"), # type: ignore
biopython_abif_raw.get("RUND4"), # type: ignore
biopython_abif_raw.get("RunN1"), # type: ignore
biopython_abif_raw.get("RUNT1"), # type: ignore
biopython_abif_raw.get("RUNT2"), # type: ignore
biopython_abif_raw.get("RUNT3"), # type: ignore
biopython_abif_raw.get("RUNT4"), # type: ignore
biopython_abif_raw.get("Satd"), # type: ignore
biopython_abif_raw.get("Scal1"), # type: ignore
biopython_abif_raw.get("SCAN1"), # type: ignore
biopython_abif_raw.get("SMED1"), # type: ignore
biopython_abif_raw.get("SMLt"), # type: ignore
biopython_abif_raw.get("SMPL1"), # type: ignore
biopython_abif_raw.get("SVER1"), # type: ignore
biopython_abif_raw.get("SVER3"), # type: ignore
biopython_abif_raw.get("Tmpr1"), # type: ignore
biopython_abif_raw.get("TUBE"), # type: ignore
biopython_abif_raw.get("User") # type: ignore
)
return trace_data
def _biopython_local_pairwise_alignment(reference: NamedString, query: NamedString) -> tuple[NamedString, NamedString]:
aligner = Align.PairwiseAligner(scoring="blastn")
aligner.mode = "local"
alignment_result = sorted(aligner.align(reference.sequence, query.sequence))[0] # take the best alignment
alignment_result = sorted(aligner.align(reference.sequence, query.sequence))[
0] # take the best alignment
return NamedString(alignment_result.sequences[0].id, alignment_result.sequences[0].seq), NamedString(alignment_result.sequences[1].id, alignment_result.sequences[1].seq)
async def reference_consensus_assembly(reference: NamedString, sanger_traces: Collection[SangerTraceData]) -> AsyncGenerator[NamedString, Any]:
for sanger_trace in sanger_traces:
yield (await asyncio.to_thread(_biopython_local_pairwise_alignment, reference, sanger_trace))[1]
yield (await asyncio.to_thread(_biopython_local_pairwise_alignment, reference, sanger_trace))[1]

10
src/automlst/engine/remote/databases/institutpasteur/mlst.py
View File

@@ -30,15 +30,11 @@ class InstitutPasteurProfiler(MLSTProfiler):
alelle_id = allele["allele_id"]
yield Allele(allele_loci=allele_loci, allele_variant=alelle_id)
async def fetch_mlst_st(self, schema_id: int, alleles: Union[AsyncIterable[Allele], Iterable[Allele]]) -> MLSTProfile:
async def fetch_mlst_st(self, schema_id: int, alleles: AsyncIterable[Allele]) -> MLSTProfile:
uri_path = f"schemes/{schema_id}/designations"
allele_request_dict: dict[str, list[dict[str, str]]] = defaultdict(list)
if isinstance(alleles, AsyncIterable):
async for allele in alleles:
allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
else:
for allele in alleles:
allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
async for allele in alleles:
allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
response = await self._http_client.post(uri_path, json={
"designations": allele_request_dict
})

2
src/automlst/engine/remote/databases/mlst.py
View File

@@ -1,6 +1,6 @@
from abc import abstractmethod
from contextlib import AbstractAsyncContextManager
from typing import AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping, Union
from typing import Any, AsyncGenerator, AsyncIterable, Generator, Iterable, Mapping, Union
from aiohttp import ClientSession