Removed unused code

src/automlst/engine/annotate.py

@@ -1,44 +0,0 @@
-import asyncio
-from collections.abc import Set
-from typing import Any, Generator, List, Sequence
-from Bio.Align import PairwiseAligner
-from Bio import Entrez
-from Bio import SeqIO
-import numpy as np
-
-from automlst.engine.data.genomics import AnnotatedString, StringAnnotation
-from automlst.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
-
-
-async def annotate_from_genbank(genbank_id: str, query_name: str, query_string: str, max_annotation_length:int = 512, gene_targets:Set = set()):
-    # TODO implement asynchronous alignment algorithm
-    reference_annotations = await fetch_ncbi_genbank(genbank_id=genbank_id)
-    query_annotations = list()
-    aligner = PairwiseAligner("blastn")
-    aligner.mode = "local"
-    for annotation in reference_annotations.annotations:
-        if annotation.type != "gene" or "gene" not in annotation.feature_properties:
-            continue
-        if len(gene_targets) > 0 and "gene" in annotation.feature_properties:
-            if not annotation.feature_properties["gene"].intersection(gene_targets):
-                continue
-        if max_annotation_length > 0 and annotation.end - annotation.start > max_annotation_length:
-            # TODO implement a failsafe
-            continue
-        feature_string_sequence = get_feature_coding(annotated_string=reference_annotations, string_annotation=annotation)
-        alignments = aligner.align(query_string, feature_string_sequence)
-        if len(alignments) < 1:
-            # TODO implement a failsafe
-            continue
-        top_alignment = sorted(alignments)[0]
-        # TODO Check if alternatives are better
-        query_annotations.append(StringAnnotation(
-            type=annotation.type, # same as original
-            start=np.min(top_alignment.aligned[0]), # We only care about the start of first chunk
-            end=np.max(top_alignment.aligned[0]), # and the end of the last chunk
-            feature_properties=dict(annotation.feature_properties) # same as original
-        ))
-    return AnnotatedString(name=query_name, sequence=query_string, annotations=query_annotations)
-
-def get_feature_coding(annotated_string: AnnotatedString, string_annotation: StringAnnotation) -> str:
-    return annotated_string.sequence[string_annotation.start:string_annotation.end]