From a637889f13c2151303998e411dc81f3196a974f6 Mon Sep 17 00:00:00 2001
From: hakangunturkun
Date: Mon, 7 Sep 2020 22:35:17 -0500
Subject: last version

---
 utility/topGene_step2_cnt_sentences.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'utility/topGene_step2_cnt_sentences.py')

diff --git a/utility/topGene_step2_cnt_sentences.py b/utility/topGene_step2_cnt_sentences.py
index b05aa7a..9791fef 100755
--- a/utility/topGene_step2_cnt_sentences.py
+++ b/utility/topGene_step2_cnt_sentences.py
@@ -12,7 +12,7 @@ def findWholeWord(w):
     return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search
 
 def getSentences(query, genes):
-    abstracts = os.popen("esearch -db pubmed -query " +  query + " | efetch -format uid |fetch-pubmed -path /run/media/hao/PubMed/Archive/ | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
+    abstracts = os.popen("esearch -db pubmed -query " +  query + " | efetch -format uid |fetch-pubmed  | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
     gene_syno=genes.split("|")
     symb=gene_syno[0]
     out=str()
-- 
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