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#!/bin/env python3
from flask import Flask, render_template, request, session, Response
import tempfile
import random
import string
from ratspub import *
import time
import os
app=Flask(__name__)
app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
@app.route("/")
def root():
return render_template('index.html')
@app.route("/about")
def about():
return render_template('about.html')
@app.route('/progress')
def progress():
# only 1-6 terms are allowed
genes=request.args.get('query')
genes=genes.replace(",", " ")
genes=genes.replace(";", " ")
genes=genes.split()
if len(genes)>=160:
message="<span class='text-danger'>Up to five terms can be searched at a time</span>"
return render_template('index.html', message=message)
elif len(genes)==0:
message="<span class='text-danger'>Please enter a search term </span>"
return render_template('index.html', message=message)
# put the query in session cookie
session['query']=genes
# 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')
@app.route("/search")
def search():
genes=session['query']
percent=round(100/(len(genes)*4),1)
snt_file=session['path']+"_snt"
cysdata=open(session['path']+"_cy","w+")
sntdata=open(snt_file,"w+")
zeroLinkNode=open(session['path']+"_0link","w+")
def generate(genes, tf_name):
sentences=str()
edges=str()
nodes=default_nodes
progress=0
searchCnt=0
nodesToHide=str()
for gene in genes:
gene=gene.replace("-"," ")
# report progress immediately
progress+=percent
yield "data:"+str(progress)+"\n\n"
#addiction terms must present with at least one drug
addiction=undic(addiction_d) +") AND ("+undic(drug_d)
sent0=gene_category(gene, addiction_d, addiction, "addiction")
e0=generate_edges(sent0, tf_name)
#
function=undic(function_d)
sent1=gene_category(gene, function_d, function, "function")
progress+=percent
yield "data:"+str(progress)+"\n\n"
e1=generate_edges(sent1, tf_name)
#
drug=undic(drug_d)
sent2=gene_category(gene, drug_d, drug, "drug")
progress+=percent
yield "data:"+str(progress)+"\n\n"
e2=generate_edges(sent2, tf_name)
# brain has its own query terms that does not include the many short acronyms
sent3=gene_category(gene, brain_d, brain_query_term, "brain")
progress+=percent
e3=generate_edges(sent3, tf_name)
geneEdges=e0+e1+e2+e3
if len(geneEdges) >1:
edges+=geneEdges
nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n"
else:
nodesToHide+=gene + " "
sentences+=sent0+sent1+sent2+sent3
#save data before the last yield
searchCnt+=1
if (searchCnt==len(genes)):
progress=100
sntdata.write(sentences)
sntdata.close()
cysdata.write(nodes+edges)
cysdata.close()
zeroLinkNode.write(nodesToHide)
zeroLinkNode.close()
yield "data:"+str(progress)+"\n\n"
return Response(generate(genes, snt_file), mimetype='text/event-stream')
@app.route('/cytoscape')
def cytoscape():
message2="This graph is interactive: <li>Click on a line to see the sentences <i>in a new window</i><li> Click on a gene to search its relations with top 150 addiction genes<li>Click on a keyword to see the terms included in the search <i> in a new window</i><p>"
with open(session['path']+"_cy","r") as f:
elements=f.read()
with open(session['path']+"_0link","r") as z:
zeroLink=z.read()
if (len(zeroLink)>0):
message2+="<span style=\"color:darkred;\">No result was found for these genes: " + zeroLink + "</span>"
return render_template('cytoscape.html', elements=elements, message="Gene vs Keywords", message2=message2)
@app.route("/sentences")
def sentences():
edge=request.args.get('edgeID')
(tf_name, gene0, cat0)=edge.split("|")
out="<h3>"+gene0 + " and " + cat0 + "</h3><hr>\n"
with open(tf_name, "r") as df:
all_sents=df.read()
for sent in all_sents.split("\n"):
if len(sent.strip())!=0:
(gene,nouse,cat, pmid, text)=sent.split("\t")
if (gene == gene0 and cat == cat0) :
out+= "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>"
return render_template('sentences.html', sentences="<ol>"+out+"</ol><p>")
## show the cytoscape graph for one gene from the top gene list
@app.route("/showTopGene")
def showTopGene():
topGene=request.args.get('topGene')
topGeneSentFile="gene_addiction_sentences_cnt.tab"
with open(topGeneSentFile, "r") as sents:
catCnt={}
for sent in sents:
(symb, cat0, cat1, pmid, sent)=sent.split("\t")
if (symb == topGene) :
if cat1 in catCnt.keys():
catCnt[cat1]+=1
else:
catCnt[cat1]=1
nodes= "{ data: { id: '" + topGene + "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+topGene+"' } },\n"
edges=str()
for key in catCnt.keys():
if ( key in drug_d.keys()):
nc=nodecolor["drug"]
else:
nc=nodecolor["addiction"]
nodes += "{ data: { id: '" + key + "', nodecolor: '" + nc + "', nodetype: 'top150', url:'/shownode?node="+key+"' } },\n"
edgeID=topGeneSentFile+"|"+topGene+"|"+key
edges+="{ data: { id: '" + edgeID+ "', source: '" + topGene + "', target: '" + key + "', sentCnt: " + str(catCnt[key]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n"
message2="<li><strong>"+topGene + "</strong> is one of the top addiction genes. <li> An archived search is shown. Click on the blue circle to update the results and include keywords for brain region and gene function. <strong> The update may take a long time to finish.</strong> "
return render_template("cytoscape.html", elements=nodes+edges, message="Top addiction genes", message2=message2)
@app.route("/shownode")
def shownode():
node=request.args.get('node')
allnodes={**brain_d, **drug_d, **function_d, **addiction_d}
out="<p>"+node.upper()+"<hr><li>"+ allnodes[node].replace("|", "<li>")
return render_template('sentences.html', sentences=out+"<p>")
@app.route("/gene_gene")
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()
os.system("rm "+tmp_ggPMID)
topGenes=dict()
out=str()
hitGenes=dict()
with open("./top_150_genes_symb_alias.txt", "r") as top_f:
for line in top_f:
(symb, alias)=line.strip().split("\t")
topGenes[symb]=alias
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:
if findWholeWord(topGenes[symb])(sent) :
sent=sent.replace("<b>","").replace("</b>","")
sent=re.sub(r'\b(%s)\b' % topGenes[symb], 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()
nodecolor={'query':"#E74C3C", 'top150': "#ccd1d1"}
nodes= "{ data: { id: '" + query + "', nodecolor: '" + nodecolor['query'] + "', nodetype: 'ggquery', fontweight:700} },\n"
edges=str()
for key in hitGenes.keys():
#nodes += "{ data: { id: '" + key + "', nodecolor: '" + nodecolor['top150'] + "', nodetype: 'top150', fontcolor:'#F2D7D5', url:'/shownode?nodetype=top150&node="+key+"' } },\n"
nodes += "{ data: { id: '" + key + "', nodecolor: '" + nodecolor['top150'] + "', nodetype: 'top150', url:'/showTopGene?topGene="+key+"' } },\n"
edgeID=gg_file+"|"+query+"|"+key
edges+="{ data: { id: '" + edgeID+ "', source: '" + query + "', target: '" + key + "', sentCnt: " + str(hitGenes[key]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n"
return render_template("cytoscape.html", elements=nodes+edges, message="Gene vs top addiction genes", message2="<li>Top addiction genes are shown in grey. <li>Click on a grey gene will show an archived search. <li>Click on the lines will show gene-gene relations <i>in a new window</i>")
## generate a page that lists all the top 150 addiction genes with links to cytoscape graph.
@app.route("/allTopGenes")
def top150genes():
return render_template("topAddictionGene.html")
if __name__ == '__main__':
app.run(debug=True)
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