map_accession_strings.py

import json

from Bio import Entrez
from django.conf import settings
from django.core.management import BaseCommand


class Command(BaseCommand):
    help = 'For every protein ID we want to search against,\
        query the NCBI database for its corresponding accession string.'

    def handle(self, *args, **options):
        protein_ids = settings.PROTEIN_ACCESSION_STRINGS_TO_IDS.values()

        # TODO: replace with API key stored as environment variable.
        Entrez.email = 'ncbi@junkinbo.xyz'

        searchHandle = Entrez.esearch(db='nucleotide', term='OR '.join([
            protein_id + '[accession]' for protein_id in protein_ids
        ]))

        ids = Entrez.read(searchHandle)['IdList']

        summary_response = Entrez.esummary(
            db='nucleotide', id=','.join(ids), retmode='json'
        )
        summary_dict = json.loads(
            summary_response.read().decode('UTF-8').strip()
        )

        for result_key in summary_dict['result']:
            if result_key == 'uids':
                continue

            hit = summary_dict['result'][result_key]
            print(hit['assemblyacc'], '=>', hit['caption'])