Get the country field for the given nuccore accession numbers.

country_from_nuccore_accessions.py

from Bio import Entrez

# Read the accessions from a file
accessions_file = 'accessions.txt'
with open(accessions_file) as f:
    ids = f.read().split('\n')

# Fetch the entries from Entrez
Entrez.email = '[email protected]'  # Insert your email here
handle = Entrez.efetch('nuccore', id=ids, retmode='xml')
response = Entrez.read(handle)

# Parse the entries to get the country
def extract_countries(entry):
    sources = [feature for feature in entry['GBSeq_feature-table']
               if feature['GBFeature_key'] == 'source']

    for source in sources:
        qualifiers = [qual for qual in source['GBFeature_quals']
                      if qual['GBQualifier_name'] == 'country']
        
        for qualifier in qualifiers:
            yield qualifier['GBQualifier_value']

for entry in response:
    accession = entry['GBSeq_primary-accession']
    for country in extract_countries(entry):
        print(accession, country, sep=',')

Funciona en Python 3, el error en el print debe ser porque lo estás corriendo con Python 2.

Justo, era eso. Gracias :)

Hello, I have used parts of this code to extract the country information for my accessions. However, where there is no country entry it is just omitting the accession. How can I use this code / alter it so it includes the accessions without a country entry in the output?

Thanks

@JackCrook If I understood correctly, you just need to add a print(accession) before the for country in ... line

super cool script! Thank you so much!!!