ncbi_get_geo_loc.py

ncbi_get_geo_loc.py

#!/usr/bin/env python
# encoding: utf-8
"""
Created by Brant Faircloth on December 17, 2025 at 14:09:15 CST
Copyright (c) 2025 Brant C. Faircloth. All rights reserved.

Description: 

"""

from Bio import Entrez
import time

Entrez.email = "you@somewhere.whatever"

seq = ["JQ688273.1","JQ688272.1","JQ688271.1"]

for iden in seq:
    handle = Entrez.efetch(db="nucleotide", id=iden, rettype="gb", retmode="XML")
    record = Entrez.read(handle)
    name = record[0]["GBSeq_accession-version"]
    location = ""
    isolate = ""
    for item in record[0]['GBSeq_feature-table'][0]['GBFeature_quals']:
        if item["GBQualifier_name"]=="geo_loc_name":
            location = (item["GBQualifier_value"])
        if item["GBQualifier_name"]=="isolate":
            isolate = (item["GBQualifier_value"])
    print(f"{name},{location},{isolate}")
    handle.close()
    time.sleep(0.5)