diff options
Diffstat (limited to 'server.py')
| -rwxr-xr-x | server.py | 132 |
1 files changed, 83 insertions, 49 deletions
@@ -36,7 +36,7 @@ def progress(): # generate a unique session ID to track the results tf_path=tempfile.gettempdir() session['path']=tf_path+"/tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6)) - return render_template('progress.html') + return render_template('progress.html', url_in="search", url_out="cytoscape") @app.route("/search") def search(): @@ -81,9 +81,10 @@ def search(): # gwas e4=searchArchived('gwas', gene) geneEdges=e0+e1+e2+e3+e4 + ## there is a bug here. zero link notes are not excluded anymore if len(geneEdges) >1: edges+=geneEdges - nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n" + nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/startGeneGene?forTopGene="+gene+"'} },\n" else: nodesToHide+=gene + " " sentences+=sent0+sent1+sent2+sent3 @@ -140,56 +141,89 @@ def shownode(): out="<p>"+node.upper()+"<hr><li>"+ allnodes[node].replace("|", "<li>") return render_template('sentences.html', sentences=out+"<p>") -@app.route("/gene_gene") +@app.route("/startGeneGene") +def startGeneGene(): + session['forTopGene']=request.args.get('forTopGene') + return render_template('progress.html', url_in="searchGeneGene", url_out="showGeneTopGene") + +@app.route("/searchGeneGene") 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 topGene_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() - hitGenes=dict() - with open("./topGene_symb_alias.txt", "r") as top_f: - for line in top_f: - (symb, alias)=line.strip().split("\t") - topGenes[symb]=alias.replace("; ","|") - for row in abstracts.split("\n"): - tiab=row.split("\t") - pmid = tiab.pop(0) - tiab= " ".join(tiab) - sentences = sent_tokenize(tiab) - ## keep the sentence only if it contains the gene - for sent in sentences: - if findWholeWord(query)(sent): - sent=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent, flags=re.I) - for symb in topGenes: - allNames=symb+"|"+topGenes[symb] - if findWholeWord(allNames)(sent) : - sent=sent.replace("<b>","").replace("</b>","") - sent=re.sub(r'\b(%s)\b' % allNames, r'<b>\1</b>', sent, flags=re.I) - out+=query+"\t"+"gene\t" + symb+"\t"+pmid+"\t"+sent+"\n" - if symb in hitGenes.keys(): - hitGenes[symb]+=1 - else: - hitGenes[symb]=1 gg_file=session['path']+"_ggSent" #gene_gene - with open(gg_file, "w+") as gg: - gg.write(out) - gg.close() - results="<h4>"+query+" vs top addiction genes</h4> Click on the number of sentences will show those sentences. Click on the <span style=\"background-color:#FcF3cf\">top addiction genes</span> will show an archived search for that gene.<hr>" - topGeneHits={} - for key in hitGenes.keys(): - url=gg_file+"|"+query+"|"+key - if hitGenes[key]==1: - sentword="sentence" - else: - sentword="sentences" - topGeneHits[ "<li> <a href=/sentences?edgeID=" + url+ " target=_new>" + "Show " + str(hitGenes[key]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key+" target=_gene><span style=\"background-color:#FcF3cf\">"+key+"</span></a>" ]=hitGenes[key] - topSorted = [(k, topGeneHits[k]) for k in sorted(topGeneHits, key=topGeneHits.get, reverse=True)] - for k,v in topSorted: - results+=k - return render_template("sentences.html", sentences=results+"<p><br>") + result_file=session['path']+"_ggResult" + def generate(query): + progress=1 + yield "data:"+str(progress)+"\n\n" + os.system("esearch -db pubmed -query \"" + query + "\" | efetch -format uid |sort >" + tmp_ggPMID) + abstracts=os.popen("comm -1 -2 topGene_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) + progress=10 + yield "data:"+str(progress)+"\n\n" + topGenes=dict() + out=str() + hitGenes=dict() + with open("topGene_symb_alias.txt", "r") as top_f: + for line in top_f: + (symb, alias)=line.strip().split("\t") + topGenes[symb]=alias.replace("; ","|") + allAbstracts= abstracts.split("\n") + abstractCnt=len(allAbstracts) + rowCnt=0 + for row in allAbstracts: + rowCnt+=1 + if rowCnt/10==int(rowCnt/10): + progress=10+round(rowCnt/abstractCnt,2)*80 + yield "data:"+str(progress)+"\n\n" + tiab=row.split("\t") + pmid = tiab.pop(0) + tiab= " ".join(tiab) + sentences = sent_tokenize(tiab) + ## keep the sentence only if it contains the gene + for sent in sentences: + if findWholeWord(query)(sent): + sent=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent, flags=re.I) + for symb in topGenes: + allNames=symb+"|"+topGenes[symb] + if findWholeWord(allNames)(sent) : + sent=sent.replace("<b>","").replace("</b>","") + sent=re.sub(r'\b(%s)\b' % allNames, r'<b>\1</b>', sent, flags=re.I) + out+=query+"\t"+"gene\t" + symb+"\t"+pmid+"\t"+sent+"\n" + if symb in hitGenes.keys(): + hitGenes[symb]+=1 + else: + hitGenes[symb]=1 + progress=95 + yield "data:"+str(progress)+"\n\n" + with open(gg_file, "w+") as gg: + gg.write(out) + gg.close() + results="<h4>"+query+" vs top addiction genes</h4> Click on the number of sentences will show those sentences. Click on the <span style=\"background-color:#FcF3cf\">top addiction genes</span> will show an archived search for that gene.<hr>" + topGeneHits={} + for key in hitGenes.keys(): + url=gg_file+"|"+query+"|"+key + if hitGenes[key]==1: + sentword="sentence" + else: + sentword="sentences" + topGeneHits[ "<li> <a href=/sentences?edgeID=" + url+ " target=_new>" + "Show " + str(hitGenes[key]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key+" target=_gene><span style=\"background-color:#FcF3cf\">"+key+"</span></a>" ]=hitGenes[key] + topSorted = [(k, topGeneHits[k]) for k in sorted(topGeneHits, key=topGeneHits.get, reverse=True)] + for k,v in topSorted: + results+=k + saveResult=open(result_file, "w+") + saveResult.write(results) + saveResult.close() + progress=100 + yield "data:"+str(progress)+"\n\n" + ## start the run + query=session['forTopGene'] + return Response(generate(query), mimetype='text/event-stream') + +@app.route('/showGeneTopGene') +def showGeneTopGene (): + with open(session['path']+"_ggResult", "r") as result_f: + results=result_f.read() + return render_template('sentences.html', sentences=results+"<p><br>") + ## generate a page that lists all the top 150 addiction genes with links to cytoscape graph. @app.route("/allTopGenes") |