From a27e09da315f26c1b6d3357da033bc6c51c0a8b6 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Thu, 6 Feb 2025 17:11:20 +0000
Subject: [PATCH] Added code to retrieve sequences and annotations from NCBI
 GenBank

---
 src/autobigs/engine/analysis/genbank.py | 26 +++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 src/autobigs/engine/analysis/genbank.py

diff --git a/src/autobigs/engine/analysis/genbank.py b/src/autobigs/engine/analysis/genbank.py
new file mode 100644
index 0000000..8d771ad
--- /dev/null
+++ b/src/autobigs/engine/analysis/genbank.py
@@ -0,0 +1,26 @@
+import asyncio
+from contextlib import AbstractAsyncContextManager
+import tempfile
+from typing import Iterable, Union
+from Bio import Entrez
+from Bio import SeqIO
+
+from autobigs.engine.structures.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)