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| author | Hao Chen | 2019-05-16 12:24:37 -0500 |
|---|---|---|
| committer | Hao Chen | 2019-05-16 12:24:37 -0500 |
| commit | 7ca139dfe40b70db4f553d09b7010712c33207fe (patch) | |
| tree | 2f1b750e31c1649af0dc5d869a7947fee806c763 | |
| parent | eeee0e3daba8dacc7301b137f131f8673c963077 (diff) | |
| download | genecup-7ca139dfe40b70db4f553d09b7010712c33207fe.tar.gz | |
pubmed location
| -rwxr-xr-x | server.py | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/server.py b/server.py index 2ce8720..d9e3551 100755 --- a/server.py +++ b/server.py @@ -162,7 +162,7 @@ def gene_gene(): query=request.args.get("gene") tmp_ggPMID=session['path']+"_ggPMID" os.system("esearch -db pubmed -query \"" + query + "\" | efetch -format uid |sort >" + tmp_ggPMID) - abstracts=os.popen("comm -1 -2 top_150_addiction_genes_uniq.pmid " + tmp_ggPMID + " |fetch-pubmed -path /run/media/hao/PubMed/Archive/ | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read() + abstracts=os.popen("comm -1 -2 top_150_addiction_genes_uniq.pmid " + tmp_ggPMID + " |fetch-pubmed -path "+pubmed_path+ " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read() os.system("rm "+tmp_ggPMID) topGenes=dict() out=str() |