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#!/bin/env python3
import os
import sys
import re
import time
from ratspub_keywords import *
def undic(dic):
return "|".join(dic.values())
def gene_addiction_cnt(gene):
time.sleep(0.2)
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)
def removeStopWords(terms):
out=str()
for one in terms.upper().split("|"):
if one not in stopWords:
out+="|"+one
return(out[1:])
def saveStopWord(w):
with open (stopword_f,"a") as swf:
swf.write(w+"\n")
return
# either start with ncbi_gene_symb_syno_name_txid9606 for fresh new counts
# or recount the results after adding additional stopwords
if len(sys.argv)==2:
input_f=sys.argv[1]
else:
input_f="./ncbi_gene_symb_syno_name_txid9606.txt"
addiction=undic(addiction_d)
drug=undic(drug_d)
output_f=input_f.replace(".txt","_absCnt.txt")
out=open(output_f, "w+")
stopword_f="./stop_words_addiction_gene_search.txt"
with open (stopword_f, "r") as swf:
stopWords=swf.read().upper().split("\n")
swf.close()
with open (input_f, "r") as f:
for line in f:
rerun=0
count=-1
inputline=line
if "'" in line:
words=line.split("|")
line=str()
for word in words:
# ' is used to mark/annotate a word is a stop word in the results
if "'" in word:
word=word.replace("'","")
stopWords.append(word)
saveStopWord(word)
rerun=1
# remove the ' mark
line+="|"+word
line=line[1:]
line=removeStopWords(line)
# tab is added if there are abstracts counts
if "\t" in line:
(gene, count)=line.split("\t")
else:
gene=line.strip()
# remove synonyms with only two letters
if "|" in gene:
synos=gene.split("|")
gene=str()
for syno in synos:
if len(syno)>2:
gene+="|"+syno
gene=gene[1:]
gene_q=gene.replace("|", "\"[tiab] OR \"")
gene_q+="[tiab]"
if rerun==1 or count== -1 :
count=gene_addiction_cnt(gene_q)
print("original line->\t"+inputline.strip())
print("stopword rmed->\t"+line.strip())
print("final result->\t"+gene+"\t"+count)
# only save the non_zero results
if (int(count)>0):
out.write(gene+"\t"+count)
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