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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]
mincnt=10
else:
input_f="./ncbi_gene_symb_syno_name_txid9606.txt"
mincnt=0;
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:
do_search=0
skip=0
inputline=line
line=line.replace("-","\ ")
# remove the annotated stopword
if re.findall(r"^xx", line):
print ("skip this line\n")
skip=1
elif "'" in line:
do_search=1
words=line.split("|")
line=str()
for word in words:
# ' is used to mark/annotate a word is a stop word in the results
# remove the ' mark
if "'" in word:
word=word.replace("'","")
stopWords.append(word)
saveStopWord(word)
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")
# rerun if count > 20; save time on reruns
if int(count)>=20:
do_search=1
else:
#no count,
gene=line.strip()
do_search=1
if do_search==1 and skip==0:
# remove synonyms with only two letters
if "|" in gene:
synos=gene.split("|")
# keep the gene name regardless number of characters
gene=synos[0]
#print ("gene: "+gene + " synos -->" + str(synos[1:]))
for syno in synos[1:]:
#synonyms must be at least 3 characters
if len(syno)>3:
gene+="|"+syno
gene_q=gene.replace("|", "\"[tiab] OR \"")
gene_q+="[tiab]"
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)
out.write(gene+"\t"+count)
else:
print("original resl->\t"+inputline.strip())
out.write(inputline)
sorted_f=output_f.replace(".txt","_sorted.txt")
os.system("sort -k2 -t$'\t' -rn " + output_f + " > " + sorted_f )
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