From 6f59cd431b1fba5fe06a6687c78f991878562d61 Mon Sep 17 00:00:00 2001 From: Jonathan DeMasi Date: Tue, 18 Jun 2019 12:09:24 -0600 Subject: added helper functions --- ncbi/dbsnp/ncbiutils.py | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100755 ncbi/dbsnp/ncbiutils.py diff --git a/ncbi/dbsnp/ncbiutils.py b/ncbi/dbsnp/ncbiutils.py new file mode 100755 index 0000000..8fb998b --- /dev/null +++ b/ncbi/dbsnp/ncbiutils.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python3 + +import requests + +BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" + +# Example https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=snp_pubmed_cited[sb]&retmax=200000&retstart=1000&retmode=json +def db_query(**kwargs): + args = [] + for key, value in kwargs.items(): + args.append(key+"="+str(value)) + qstring = "&".join(args) + print(qstring) + resp = requests.get(BASE_URL + qstring) + if resp.status_code == 200: + results = resp.json() + return(results) + else: + print("You've encountered an error and we can't return your results") + +def main(): + results = db_query(db="snp", term="snp_pubmed_cited[sb]", retmax=200000, retstart=1000, retmode="json") + print(results) + return() + +if __name__ == '__main__': + main() \ No newline at end of file -- cgit v1.2.3