fetching results

1 files changed, 37 insertions, 0 deletions

diff --git a/ncbi/dbsnp/dbsnp.py b/ncbi/dbsnp/dbsnp.py
index e5a0d9b..fbad492 100644..100755
--- a/ncbi/dbsnp/dbsnp.py
+++ b/ncbi/dbsnp/dbsnp.py
@@ -1 +1,38 @@
 #!/usr/bin/env python3
+
+import sys
+import time
+from Bio import Entrez
+
+
+Entrez.email = "jonathan.demasi@colorado.edu"
+# We should apply for an API key so we get more queries/sec
+Entrez.api_key = None
+
+def get_complete_rsids():
+    rsidlist = []
+    numresults = 0
+    retstart = 0
+    search_string = "snp_pubmed_cited[sb]"
+    search_results = Entrez.read(Entrez.esearch(db="snp", term=search_string,
+                                                retmax=100000, retstart=retstart, usehistory="y"))
+    print("Found a total of " +
+          search_results["Count"] + " results using search string '" + search_string + "'")
+    numresults = search_results["Count"]
+    rsidlist = rsidlist + search_results["IdList"]
+    additional_queries = int(int(numresults) / 100000)
+    while additional_queries != 0:
+        retstart = retstart + 100000
+        search_results = Entrez.read(Entrez.esearch(db="snp", term=search_string,
+                                                    retmax=100000, retstart=retstart, usehistory="y"))
+        rsidlist = rsidlist + search_results["IdList"]
+        additional_queries = additional_queries - 1
+    return(rsidlist)
+
+def main():
+    listy = get_complete_rsids()
+    return()
+
+if __name__ == '__main__':
+    main()
+