add a few more opiods

2 files changed, 34 insertions, 1 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)
+
diff --git a/ratspub.py b/ratspub.py
index dd20f67..70877b6 100755
--- a/ratspub.py
+++ b/ratspub.py
@@ -105,7 +105,7 @@ addiction=undic(addiction_d)
 drug_d = {"alcohol":"alcohol|alcoholism|alcoholic",
         "nicotine":"smoking|nicotine|tobacco",
         "cocaine":"cocaine",
-        "opioid":"opioid|opioids|fentanyl|oxycodone|oxycontin|heroin|morphine|methadone|buprenorphine",
+        "opioid":"opioid|opioids|fentanyl|oxycodone|oxycontin|heroin|morphine|methadone|buprenorphine|vicodin|hydrocodone|hycodan|kadian|percoset|hydromorphone|naloxone|codeine|suboxone|tramadol|kratom",
         "amphetamine":"methamphetamine|amphetamine|METH",
         "cannabinoid":"endocannabinoid|cannabinoids|endocannabinoids|marijuana|cannabidiol|cannabinoid|tetrahydrocannabinol|thc|thc 9|Oleoylethanolamide|palmitoylethanolamide|acylethanolamides"
         }