27 lines
1.1 KiB
Python

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)