step 1 in topgene

1 files changed, 37 insertions, 0 deletions

diff --git a/topGene_step1_cnt_abstracts.py b/topGene_step1_cnt_abstracts.py
new file mode 100755
index 0000000..0880aff
--- /dev/null
+++ b/topGene_step1_cnt_abstracts.py
@@ -0,0 +1,37 @@
+#!/bin/env python3 
+import os
+import re
+import time
+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)
+        return gene_addiction_cnt(gene)
+    else:
+        return (count)
+
+out=open("gene_addiction_abstract_cnt_result.tab", "w+")
+
+with open ("./ncbi_gene_symb_syno_name_txid9606.txt", "r") as f:
+    for line in f:
+        line=re.sub(r"\)|\(|\[|\]|\*|\'","",line.strip())
+        if "\t" in line:
+            (gene, synostring)=line.strip().split("\t")
+            if "|" in synostring:
+                synos=synostring.split("|") 
+            elif len(synostring)>3:
+                synos=synostring
+            for syno in synos:
+                if len(syno)>3:
+                    gene+="|"+syno
+        else:
+            gene=line.strip()
+        gene_q=gene.replace("|", " [tiab] OR ")
+        gene_q+="[tiab]"
+        count=gene_addiction_cnt(gene_q)
+        print(gene+"\t"+count)
+        out.write(gene+"\t"+count)