added helper functions

1 files changed, 27 insertions, 0 deletions

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()
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