#!/usr/bin/env python3

# -*- coding: utf-8 -*-

"""

This script uses Biopython ENTREZ to retrieve and download information of interest available through NCBI.

"""

from Bio import Entrez

from tqdm import tqdm

from urllib.parse import quote

def search_pubmed(searchTerm,

email,

number):

"""Download the attribute for accessions of interest using Biopython Entrez"""

Entrez.email = email

handle = Entrez.read(Entrez.esearch(db="pubmed", term=searchTerm, retmax = number))

idList = handle["IdList"]

searchResult = []

for idTerm in tqdm(idList):

try:

esummary_handle = Entrez.esummary(db="pubmed", id=idTerm, report="full")

esummary_record = Entrez.read(esummary_handle, validate = False)

encodedDOI = quote(esummary_record[0]["DOI"], safe='')

esummary_record[0]["encodedDOI"] = encodedDOI

searchResult += esummary_record

except:

pass

return searchResult

if __name__ == '__main__':

search_pubmed("", "email", 100)