diff options
Diffstat (limited to 'utility/topGene_step2_cnt_sentences.py')
| -rwxr-xr-x | utility/topGene_step2_cnt_sentences.py | 2 |
1 files changed, 1 insertions, 1 deletions
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() |