feat(IPVC-3047): script for pulling gbff files from NCBI per accession

sbin/download_ncbi_gbff.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+
+import argparse
+import logging.config
+
+import importlib_resources
+
+from uta.tools.eutils import download_from_eutils, NcbiFileFormatEnum
+
+logging_conf_fn = importlib_resources.files("uta").joinpath("etc/logging.conf")
+logging.config.fileConfig(logging_conf_fn)
+logging.getLogger().setLevel(logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+def download_transcript_gbff_from_ncbi(transcript_ac_file_path: str, output_dir: str) -> None:
+    with open(transcript_ac_file_path) as f:
+        for line in f:
+            transcript_ac = line.strip()
+            logger.info(f"Downloading GenBank file for transcript {transcript_ac}")
+            ac_file_path = f"{output_dir}/{transcript_ac}.gbff"
+            download_from_eutils(transcript_ac, NcbiFileFormatEnum.GENBANK, ac_file_path)
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Download GenBank files from NCBI.')
+    parser.add_argument("transcript_ac_file_path", type=str)
+    parser.add_argument("--output-dir", "-o", default=".", type=str)
+    args = parser.parse_args()
+
+    logger.info("Downloading GenBank files from NCBI")
+    download_transcript_gbff_from_ncbi(args.transcript_ac_file_path, args.output_dir)
+
+
+if __name__ == "__main__":
+    main()