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=',')

Hola,
He tratado de usar tu script, meto mi archivo con sólo los números de acceso como mencionas en el foro, pero al correrlo me sale un error de sintaxis en la ultima linea: "print(accession, country, sep=',')" . Sabes a qué se podría deber?
Muchas gracias
Saludos

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!!!