From ff4514b3d51455bd592e038faa8cdb7516469a99 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 7 May 2019 15:44:11 -0500
Subject: Fixed issue where, if the user searched for a location range in the
 SNP Browser, it often wouldn't correctly identify when markers were on genes

---
 wqflask/wqflask/snp_browser/snp_browser.py | 26 +++++++++++++++++++++++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 360e6b28..9a980cb1 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -300,7 +300,7 @@ class SnpBrowser(object):
                             gene_id = get_gene_id(self.species_id, self.gene_name)
                             gene = [gene_id, self.gene_name]
                         else:
-                            gene = ""
+                            gene = check_if_in_gene(species_id, chr, mb)
                         transcript = exon = function = function_details = ''
                         if self.redundant == "false" or last_mb != mb: # filter redundant
                             if self.include_record(domain, function, snp_source, conservation_score):
@@ -444,8 +444,8 @@ class SnpBrowser(object):
                 if domain:
                     domain_1 = domain[0]
                     domain_2 = domain[1]
-                    if domain_1 == "Intergenic" and self.gene_name != "":
-                        domain_1 = self.gene_name
+                    if domain_1 == "Intergenic" and gene != "":
+                        domain_1 = gene_name
                     else:
                         if domain_1 == "Exon":
                             domain_1 = domain_1 + " " + exon
@@ -874,3 +874,23 @@ def get_gene_id_name_dict(species_id, gene_name_list):
         pass
 
     return gene_id_name_dict
+
+def check_if_in_gene(species_id, chr, mb):
+    if species_id != 0: #ZS: Check if this is necessary
+        query = """SELECT geneId, geneSymbol
+                   FROM GeneList
+                   WHERE SpeciesId = {0} AND chromosome = '{1}' AND
+                        (txStart < {2} AND txEnd > {2}); """.format(species_id, chr, mb)
+    else:
+        query = """SELECT geneId,geneSymbol
+                   FROM GeneList
+                   WHERE chromosome = '{0}' AND
+                        (txStart < {1} AND txEnd > {1}); """.format(species_id, chr, mb)
+
+    result = g.db.execute(query).fetchone()
+
+    if result:
+        return [result[0], result[1]]
+    else:
+        return ""
+
-- 
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