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Merge branch 'develop'

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This commit is contained in:
Harrison Deng 2025-01-17 14:34:16 +00:00
commit cb22dfac9b
15 changed files with 28 additions and 183 deletions
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19
Jenkinsfile vendored
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@ -30,11 +30,26 @@ pipeline {
}
}
stage("publish") {
parallel {
stage ("git.reslate.systems") {
environment {
CREDS = credentials('4d6f64be-d26d-4f95-8de3-b6a9b0beb311')
TOKEN = credentials('git.reslate.systems')
}
steps {
sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${CREDS_USR}/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
}
}
stage ("test.pypi.org") {
when {
tag '*.*'
}
environment {
TOKEN = credentials('test.pypi.org')
}
steps {
sh returnStatus: true, script: 'python -m twine upload -r testpypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
}
}
}
}
}

0
src/automlst/engine/remote/databases/ncbi/__init__.py → src/automlst/engine/data/local/__init__.py
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2
src/automlst/engine/local/csv.py → src/automlst/engine/data/local/csv.py
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@ -3,7 +3,7 @@ from io import TextIOWrapper
from os import PathLike
from typing import AsyncIterable, Iterable, Mapping, Sequence, Union
from automlst.engine.data.mlst import Allele, MLSTProfile
from automlst.engine.data.structures.mlst import Allele, MLSTProfile
def dict_loci_alleles_variants_from_loci(alleles_map: Mapping[str, Sequence[Allele]]):

2
src/automlst/engine/local/fasta.py → src/automlst/engine/data/local/fasta.py
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@ -3,7 +3,7 @@ from io import TextIOWrapper
from typing import Any, AsyncGenerator, Generator, Iterable, Sequence, Union
from Bio import SeqIO
from automlst.engine.data.genomics import NamedString
from automlst.engine.data.structures.genomics import NamedString
async def read_fasta(handle: Union[str, TextIOWrapper]) -> AsyncGenerator[NamedString, Any]:
fasta_sequences = asyncio.to_thread(SeqIO.parse, handle=handle, format="fasta")

0
src/automlst/engine/data/remote/__init__.py Normal file
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4
src/automlst/engine/remote/databases/bigsdb.py → src/automlst/engine/data/remote/databases/bigsdb.py
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@ -5,8 +5,8 @@ from typing import Any, AsyncGenerator, AsyncIterable, Collection, Generator, It
from aiohttp import ClientSession, ClientTimeout
from automlst.engine.data.genomics import NamedString
from automlst.engine.data.mlst import Allele, PartialAllelicMatchProfile, MLSTProfile
from automlst.engine.data.structures.genomics import NamedString
from automlst.engine.data.structures.mlst import Allele, PartialAllelicMatchProfile, MLSTProfile
from automlst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException
class BIGSdbMLSTProfiler(AbstractAsyncContextManager):

0
src/automlst/engine/data/structures/__init__.py Normal file
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0
src/automlst/engine/data/genomics.py → src/automlst/engine/data/structures/genomics.py
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0
src/automlst/engine/data/mlst.py → src/automlst/engine/data/structures/mlst.py
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126
src/automlst/engine/local/abif.py
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@ -1,126 +0,0 @@
import asyncio
from numbers import Number
from os import path
from typing import Any, AsyncGenerator, Collection, Iterable, Sequence, Union
from automlst.engine.data.genomics import NamedString, SangerTraceData
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO, Align
from automlst.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
def _biopython_read_abif_sequence(seq_path: str) -> SeqRecord:
with open(seq_path, "rb") as seq_handle:
return SeqIO.read(seq_handle, "abi")
async def read_abif(seq_path: str) -> SangerTraceData:
ext = path.splitext(seq_path)[1]
if ext.lower() != ".ab1" and ext.lower() != "abi":
raise ValueError(
'seq_path must have file extension of "ab1", or "abi".')
biopython_seq = await asyncio.to_thread(_biopython_read_abif_sequence, seq_path)
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
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
)
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
# TODO actually assemble the consensus sequence here
raise NotImplementedError("Pairwise alignment unto reference consensus assembly function not ready.")
async def reference_consensus_assembly(reference: Union[NamedString, str], sanger_traces: Iterable[SangerTraceData]) -> AsyncGenerator[NamedString, Any]:
if isinstance(reference, str):
reference_seq = NamedString(name=reference, sequence=(await fetch_ncbi_genbank(reference)).sequence)
else:
reference_seq: NamedString = reference
for sanger_trace in sanger_traces:
yield NamedString("NA", "NA")
raise NotImplementedError("Pairwise alignment unto reference consensus assembly function not ready.")

27
src/automlst/engine/remote/databases/ncbi/genbank.py
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@ -1,27 +0,0 @@
import asyncio
from Bio import Entrez
from Bio import SeqIO
# TODO Change this out for a more professional approach
Entrez.email = "yunyangdeng@outlook.com"
from automlst.engine.data.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)

2
tests/automlst/engine/local/test_fasta.py → tests/automlst/engine/data/local/test_fasta.py
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@ -1,4 +1,4 @@
from automlst.engine.local.fasta import read_fasta
from automlst.engine.data.local.fasta import read_fasta
async def test_fasta_reader_not_none():

6
tests/automlst/engine/remote/databases/test_bigsdb.py → tests/automlst/engine/data/remote/databases/test_bigsdb.py
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@ -3,10 +3,10 @@ import re
from typing import Collection, Sequence, Union
from Bio import SeqIO
import pytest
from automlst.engine.data.genomics import NamedString
from automlst.engine.data.mlst import Allele, MLSTProfile
from automlst.engine.data.structures.genomics import NamedString
from automlst.engine.data.structures.mlst import Allele, MLSTProfile
from automlst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException
from automlst.engine.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler
from automlst.engine.data.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler
def gene_scrambler(gene: str, mutation_site_count: Union[int, float], alphabet: Sequence[str] = ["A", "T", "C", "G"]):
rand = random.Random(gene)

12
tests/automlst/engine/local/test_abif.py
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@ -1,12 +0,0 @@
import os
from automlst.engine.local.abif import read_abif, reference_consensus_assembly
async def test_load_sanger_sequence_has_data():
assert os.path.exists("tests/resources/1I1_F_P1815443_047.ab1")
result_data = await read_abif("tests/resources/1I1_F_P1815443_047.ab1")
assert result_data is not None
async def test_consensus_assembly_with_ncbi():
consensus = reference_consensus_assembly("ON685494.1", [await read_abif("tests/resources/1I1_F_P1815443_047.ab1"), await read_abif("tests/resources/1I1_R_P1815443_094.ab1")])
# TODO complete implementing this

5
tests/automlst/engine/remote/databases/ncbi/test_genbank.py
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@ -1,5 +0,0 @@
from automlst.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
async def test_fetch_ncbi_genbank_with_id_works():
assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0