Refactored code layout

src/automlst/engine/data/local/abif.py

@@ -2,12 +2,10 @@ 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 automlst.engine.data.structures.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:
@@ -114,13 +112,3 @@ def _biopython_local_pairwise_alignment(reference: NamedString, query: NamedStri
         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.")

src/automlst/engine/data/local/csv.py

@@ -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]]):

src/automlst/engine/data/local/fasta.py

@@ -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")

src/automlst/engine/data/remote/databases/bigsdb.py

@@ -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):

tests/automlst/engine/local/test_abif.py

@@ -1,12 +1,8 @@
 import os
 
-from automlst.engine.local.abif import read_abif, reference_consensus_assembly
+from automlst.engine.data.local.abif import read_abif
 
 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

tests/automlst/engine/remote/databases/ncbi/test_genbank.py

@@ -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 

tests/automlst/engine/remote/databases/test_bigsdb.py

@@ -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)