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#!/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()
if (len(count)==0):
print("pause")
time.sleep(15)
gene_addiction_cnt(gene)
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)
print(gene+"\t"+count)
out.write(gene+"\t"+count)
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