From 5f34a35553a2c58d21096822ecb4e79c669f4521 Mon Sep 17 00:00:00 2001
From: Jonathan DeMasi <jonathan.demasi@colorado.edu>
Date: Tue, 18 Jun 2019 13:48:30 -0600
Subject: pushing all changes with working ncbiutils

---
 ncbi/dbsnp/dbsnp.py     | 75 ++++++++++++++-----------------------------------
 ncbi/dbsnp/ncbiutils.py | 11 +-------
 2 files changed, 22 insertions(+), 64 deletions(-)
 mode change 100755 => 100644 ncbi/dbsnp/ncbiutils.py

(limited to 'ncbi')

diff --git a/ncbi/dbsnp/dbsnp.py b/ncbi/dbsnp/dbsnp.py
index 9878df7..abbe326 100755
--- a/ncbi/dbsnp/dbsnp.py
+++ b/ncbi/dbsnp/dbsnp.py
@@ -1,58 +1,31 @@
 #!/usr/bin/env python3
 
 import time
+import ncbiutils
 from Bio import Entrez
-import xml.etree.ElementTree as ET
 
 
-DEBUG = True
-Entrez.email = "jonathan.demasi@colorado.edu"
-# We should apply for an API key so we get more queries/sec
-Entrez.api_key = None
-
+"""
+Finds all rsids that are explicitly cited in pubmed
+and returns a list
+"""
 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
+    results = ncbiutils.db_query(db="snp",retmode="json",retmax=200000,retstart=0,term='snp_pubmed_cited[sb]')
+    rsidlist = results["esearchresult"]["idlist"]
+    for x in range(0, len(rsidlist)):
+        rsidlist[x] = "rs" + rsidlist[x]
     return(rsidlist)
 
-def get_pmids(interm):
-    # This is obsolete now, essentially, but
-    # allows a user to pass a single string
-    # which can be nice.
-    if isinstance(interm, str):
-        interm = "rs" + interm + " AND pubmed_snp_cited[sb]"
-        search_results = Entrez.read(Entrez.esearch(db="pubmed", term=interm,
-                                                    retmax=100000,
-                                                    usehistory="y"))
-        print("Found a total of " +
-              search_results["Count"] + " results using search string '" + interm + "'")
-        return(search_results)
-
-    elif isinstance(interm, list):
-        searchstring = " OR ".join(interm)
-        searchstring = "(" + searchstring + ") AND pubmed_snp_cited[sb]"
-        search_results = Entrez.read(Entrez.esearch(db="pubmed",
-                                                    term=searchstring,
-                                                    retmax=100000,
-                                                    usehistory="y"))
-        print("Found a total of " +
-              search_results["Count"] + " results using search string'" + searchstring + "'")
-    return(search_results)
+"""
+Generates a list of PMIDs that are explicitly cite a given rsid
+"""
+def get_pmids(rsid):
+    searchterm = rsid + "+AND+pubmed_snp_cited[sb]"
+    print(searchterm)
+    results = ncbiutils.db_query(db="pubmed",retmode="json",retmax=200000,restart=0,term=searchterm, api_key="7c0213f7c513fa71fe2cb65b4dfefa76fb09")
+    pmidlist = results["esearchresult"]["idlist"]
+    print(pmidlist)
+    return(pmidlist)
 
 
 """
@@ -95,14 +68,8 @@ def get_abstracts_from_list(pmids_list):
 
 def main():
     rsids = get_complete_rsids()
-    if DEBUG:
-        for x in rsids:
-            print(x)
-    for x in rsids:
-        pmids = get_pmids(x)
-        abstracts = get_abstracts_from_list(pmids)
-        for thing in abstracts:
-            print(thing)
+    for rsid in rsids:
+        get_pmids(rsid)
     return()
 
 if __name__ == '__main__':
diff --git a/ncbi/dbsnp/ncbiutils.py b/ncbi/dbsnp/ncbiutils.py
old mode 100755
new mode 100644
index 8fb998b..b3c199a
--- a/ncbi/dbsnp/ncbiutils.py
+++ b/ncbi/dbsnp/ncbiutils.py
@@ -10,18 +10,9 @@ def db_query(**kwargs):
     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
+        print("You've encountered an error and we can't return your results")
\ No newline at end of file
-- 
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