From 08503676ea318ade7a72fcd999a32bc6e5433e0c Mon Sep 17 00:00:00 2001
From: Hao Chen
Date: Fri, 10 May 2019 12:52:29 -0500
Subject: re run the quey if no result

---
 cnt_gene_addiction_abstracts.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'cnt_gene_addiction_abstracts.py')

diff --git a/cnt_gene_addiction_abstracts.py b/cnt_gene_addiction_abstracts.py
index c216862..f55586f 100755
--- a/cnt_gene_addiction_abstracts.py
+++ b/cnt_gene_addiction_abstracts.py
@@ -8,6 +8,10 @@ from ratspub  import *
 def gene_addiction_cnt(gene):
     q="\"(" + addiction.replace("|", "[tiab] OR ")  + ") AND (" + drug.replace("|", "[tiab] OR ", ) + ") AND (" + gene + ")\""
     count=os.popen('esearch -db pubmed  -query ' + q + ' | xtract -pattern ENTREZ_DIRECT -element Count ').read()
+    if (len(count)==0):
+        print("pause")
+        time.sleep(15)
+        gene_addiction_cnt(gene)
     return (count)
 
 out=open("gene_addiction_cnt_result_part1.tab", "w+")
@@ -25,9 +29,6 @@ with open ("./ncbi_gene_symb_syno_txid9606_part1.txt", "r") as f:
             gene_q=gene.replace("|", " [tiab] OR ")
             gene_q+="[tiab]"
             count=gene_addiction_cnt(gene_q)
-            if (len(count)==0):
-                print("pause")
-                time.sleep(10)
             print(gene+"\t"+count)
             out.write(gene+"\t"+count)
 
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