1 files changed, 33 insertions, 0 deletions
diff --git a/cnt_gene_addiction_abstracts.py b/cnt_gene_addiction_abstracts.py
new file mode 100755
index 0000000..c216862
--- /dev/null
+++ b/cnt_gene_addiction_abstracts.py
@@ -0,0 +1,33 @@
+#!/bin/env python3 
+import os
+import re
+import time
+from ratspub  import * 
+## turn dictionary (synonyms) to regular expression
+
+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()
+    return (count)
+
+out=open("gene_addiction_cnt_result_part1.tab", "w+")
+
+cnt=0
+with open ("./ncbi_gene_symb_syno_txid9606_part1.txt", "r") as f:
+    for line in f:
+        line=re.sub(r"\)|\(|\[|\]|\*|\'","",line)
+        (gene, synoms)=line.strip().split("\t")
+        if (gene[0:3] != "LOC"):
+            cnt+=1
+            for syno in synoms.split("|"):
+                if len(syno)>3:
+                    gene+="|"+syno
+            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)
+