add EBI GWAS

5 files changed, 92 insertions, 31 deletions

diff --git a/process_gwas.py b/process_gwas.py
new file mode 100644
index 0000000..eba59c0
--- /dev/null
+++ b/process_gwas.py
@@ -0,0 +1,48 @@
+import re
+
+with open("./addiction_gwas.tsv", "r") as f:
+    for line in f:
+        try:
+            (pmid, trait0, gene0, gene1, snp, pval, trait1)=line.strip().split("\t")
+        except:
+            next
+        key1="unassigned"
+        key2="unassigned"
+        trait=trait0+"; "+trait1
+        genes=gene0+";"+gene1
+        if re.search('cocaine', trait, flags=re.I):
+            key1="addiction"
+            key2="cocaine"
+        elif re.search('smoking|congestive|nicotine', trait, flags=re.I):
+            key1="addiction"
+            key2="nicotine"
+        elif re.search('opioid|morphin|heroin|methadone', trait, flags=re.I):
+            key1="addiction"
+            key2="opioid"
+        elif re.search('amphetam', trait, flags=re.I):
+            key1="addiction"
+            key2="amphetamine"
+        elif re.search('canabis', trait, flags=re.I):
+            key1="addiction"
+            key2="canabis"
+        elif re.search('food', trait, flags=re.I):
+            key1="addiction"
+            key2="food"
+        elif re.search('alcohol', trait, flags=re.I):
+            key1="addiction"
+            key2="alcohol"
+        elif re.search('addiction|abuse', trait, flags=re.I):
+            key1="addiction"
+            key2="addiction"
+        else:
+            key1="behavior"
+            key2="psychiatric"
+        genes=genes.replace(" - ", ";")
+        genes=genes.replace(",", ";")
+        printed=dict()
+        for gene in genes.split(";"):
+            gene=gene.replace(" ","")
+            if gene !="NR" and gene not in  printed:
+                text="SNP:<b>"+snp+"</b>, P value: <b>"+pval+"</b>, Disease/trait:<b> "+trait0+"</b>, Mapped trait:<b> "+trait1+"</b>"
+                print (gene+"\t"+"GWAS"+"\t"+key2+"_GWAS\t"+pmid+"\t"+text)
+            printed[gene]=1
diff --git a/ratspub.py b/ratspub.py
index 0cc5d8a..e9a911b 100755
--- a/ratspub.py
+++ b/ratspub.py
@@ -65,13 +65,43 @@ def generate_edges(data, filename):
         json0+="{ data: { id: '" + edgeID + "', source: '" + source + "', target: '" + target + "', sentCnt: " + str(edgeCnts[edgeID]) + ",  url:'/sentences?edgeID=" + edgeID + "' } },\n"
     return(json0)
 
+def searchArchived(sets, query):
+    if sets=='topGene':
+        dataFile="topGene_addiction_sentences.tab"
+        nodes= "{ data: { id: '" + query +  "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+query+"' } },\n"
+    elif sets=='gwas':
+        dataFile="gwas_addiction.tab"
+        nodes=str()
+    with open(dataFile, "r") as sents:
+        catCnt={}
+        for sent in sents:
+            (symb, cat0, cat1, pmid, sent)=sent.split("\t")
+            if (symb.upper() == query.upper()) :
+                if cat1 in catCnt.keys():
+                    catCnt[cat1]+=1
+                else:
+                    catCnt[cat1]=1
+    nodes= "{ data: { id: '" + query +  "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+query+"' } },\n"
+    edges=str()
+    for key in catCnt.keys():
+        if sets=='gwas':
+            nc=nodecolor["gwas"]
+        elif 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=dataFile+"|"+query+"|"+key
+        edges+="{ data: { id: '" + edgeID+ "', source: '" + query + "', target: '" + key + "', sentCnt: " + str(catCnt[key]) + ",  url:'/sentences?edgeID=" + edgeID + "' } },\n"
+    return(nodes+edges)
+
 # brain region has too many short acronyms to just use the undic function, so search PubMed using the following 
 brain_query_term="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic|habenula"
 function=undic(function_d)
 addiction=undic(addiction_d)
 drug=undic(drug_d)
 
-nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7"}
+nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7", 'gwas':"#AEB6BF"}
 #https://htmlcolorcodes.com/
 n0=generate_nodes(function_d, 'function')
 n1=generate_nodes(addiction_d, 'addiction')
diff --git a/server.py b/server.py
index 62a959e..7bdd3f2 100755
--- a/server.py
+++ b/server.py
@@ -78,7 +78,9 @@ def search():
             sent3=gene_category(gene, brain_d, brain_query_term, "brain")
             progress+=percent
             e3=generate_edges(sent3, tf_name)
-            geneEdges=e0+e1+e2+e3
+            # gwas
+            e4=searchArchived('gwas', gene)
+            geneEdges=e0+e1+e2+e3+e4
             if len(geneEdges) >1:
                 edges+=geneEdges
                 nodes+="{ data: { id: '" + gene +  "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n"
@@ -119,36 +121,17 @@ def sentences():
     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) :
+           if (gene.upper() == gene0.upper() and cat.upper() == cat0.upper()) :
                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="topGene_addiction_sentences.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)
+    query=request.args.get('topGene')
+    nodesEdges=searchArchived('topGene',query)
+    message2="<li><strong>"+query + "</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=nodesEdges, message="Top addiction genes", message2=message2)
 
 @app.route("/shownode")
 def shownode():
diff --git a/templates/index.html b/templates/index.html
index f5b6aea..bbdebfa 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -8,9 +8,9 @@
 <table>
 	<tr><td >
 <p>
-	RatsPub searches PubMed to find <i>sentences</i> that contain the query terms (i.e., gene symbols) and  <a href="https://github.com/chen42/RatsPub/blob/master/ratspub_keywords.py">drug addiction-related keywords</a>.  These gene-keyword relationships are presented as an interactive graph that can efficiently  answer the question <b>"What do we know about these genes and addiction?" </b>
+			RatsPub searches PubMed to find <i>sentences</i> that contain the query terms (i.e., gene symbols) and  <a href="https://github.com/chen42/RatsPub/blob/master/ratspub_keywords.py">drug addiction-related keywords</a>.  These gene-keyword relationships are presented as an interactive graph that can efficiently  answer the question <b>"What do we know about these genes and addiction?". </b> To better answer this question, data from <a href="https://www.ebi.ac.uk/gwas/">EBI GWAS catalog </a>are also included in the search.
 
-<p> In addition, clicking gene names in the graph will launch a new search for sentences containing the target gene and 200 addiction-related genes. These results help to answer the question <b>"Are there  genes that can link my gene of interest to addiction?"  </b>
+<p> The graph has many interactive elements. For example, clicking gene names will launch a new search for sentences containing the target gene and 200 addiction-related genes. These results help to answer the question <b>"Are there  genes that can link my gene of interest to addiction?"  </b>
 		</td>
 		<td >
 			<div class='img'><img src="/static/ratspub.png" class="img-fluid">
diff --git a/templates/progress.html b/templates/progress.html
index 081f1d9..e881a90 100644
--- a/templates/progress.html
+++ b/templates/progress.html
@@ -6,9 +6,9 @@
 <script>
 
 
-var r =  Math.floor(Math.random() * Math.floor(125));
-var g =  Math.floor(Math.random() * Math.floor(125));
-var b =  Math.floor(Math.random() * Math.floor(125));
+var r =  Math.floor(Math.random() * Math.floor(100));
+var g =  Math.floor(Math.random() * Math.floor(100));
+var b =  Math.floor(Math.random() * Math.floor(100));
 document.body.style.backgroundColor = 'rgba('+r+','+g+','+b+',0.1)'
 
 var source = new EventSource("/search");