fix Multiallelic error message

LDlink/LDcommon.py

@@ -532,6 +532,7 @@ def get_query_variant_c(snp_coord, pop_ids, request, genome_build, is_output,out
     if "," in geno[3] or "," in geno[4]:
         # print('handle error: snp + " is not a biallelic variant."')
         queryVariantWarnings.append([snp_coord[0], "NA", "Variant is not a biallelic."])
+        output["error"]= snp_coord[0] + " variant is not a biallelic." + str(output["warning"] if "warning" in output else "")
 
     index = []
     for i in range(9, len(head)):

LDlink/LDhap.py

@@ -197,7 +197,12 @@ def calculate_hap(snplst, pop, request, web, genome_build):
                     alleles = a2+"="+str(round(f1, 3))+", " + \
                         a1+"="+str(round(f0, 3))
                 allele_lst.append(alleles)
-
+            else:
+                if len(snp_dict) > 1:
+                    output["warning"] = str(output["warning"] if "warning" in output else "")  + rs_input+ " variant is not a biallelic"
+                else:
+                    output["error"] = str(output["error"] if "error" in output else "")  + rs_input+ " variant is not a biallelic"
+                    return(json.dumps(output, sort_keys=True, indent=2))
     haps = {}
     for i in range(len(index)):
         h1 = "_".join(hap1[i])

LDlink/LDlink-5.5.1.js → LDlink/LDlink-5.5.2.js

@@ -1,4 +1,4 @@
-var ldlink_version = "Version 5.5.1";
+var ldlink_version = "Version 5.5.2";
 
 
 // var restService = {protocol:'http',hostname:document.location.hostname,fqn:"nci.nih.gov",port:9090,route : "LDlinkRestWeb"}
@@ -67,7 +67,7 @@ $(document).ready(function() {
     });
 
     // Load news text from news.html to news-container div
-    $.get("news-5.5.1.html", function (data) {
+    $.get("news-5.5.2.html", function (data) {
         let tmpData = data.split("<p>")
         let i = 0;
         var newsHTMLList = [];
@@ -1469,12 +1469,13 @@ function ldproxy_rs_results_link(data, type, row) {
     if(!data.includes("rs") || data.length <= 2) {
         return ".";
     }
-    var server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+    var server = 'http://www.ncbi.nlm.nih.gov/snp/';
     var rs_number = data.substring(2);
     var params = {
         rs : rs_number
     };
-    var href = server + "?" + $.param(params);
+    //var href = server + "?" + $.param(params);
+    var href = server  + data;
     var target = 'rs_number_' + Math.floor(Math.random() * (99999 - 10000 + 1));
 //  var href = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=128';
     var link;
@@ -1856,7 +1857,7 @@ function populateHeaderValues(event, numFiles, label) {
 }
 
 function loadHelp() {
-    $('#help-tab').load('help-5.5.1.html');
+    $('#help-tab').load('help-5.5.2.html');
 }
 
 function calculate(e) {
@@ -2990,14 +2991,14 @@ function populateSNPlist(data) {
 }
 
 function anchorRSnumber(rs_number) {
-    var server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
-
+    //var server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+    var server = 'http://www.ncbi.nlm.nih.gov/snp/';
     var raw_rs_number = rs_number.substring(2);
     var params = {
         rs : raw_rs_number
     };
-    var url = server + "?" + $.param(params);
-
+    //var url = server + "?" + $.param(params);
+    var url = server + rs_number;
     return '<a href="'+url+'" target="rs_number_'+rs_number+'">'+rs_number+'</a>';
 }
 
@@ -4757,7 +4758,8 @@ function addLDHapHyperLinks(request, ldhapTable) {
     $.each(ldhapTable.rows, function(index, value) {
         //console.log(index + ": " + value);
         // Create RSnumber link (Cluster Report)
-        server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+        //server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+        var server = 'http://www.ncbi.nlm.nih.gov/snp/';
         // snp1-rsum
         rs_number = value.RS.substring(2);
         params = {
@@ -4782,6 +4784,7 @@ function addLDHapHyperLinks(request, ldhapTable) {
             'hgFind.matches' : rs_number
         };
         url = server + "?" + $.param(params);
+        //url = server  + value.RS;
         $('#Coord_hap_' + index + ' a:first-child').attr('href', url);
     });
 
@@ -4797,9 +4800,12 @@ function addLDpairHyperLinks(data) {
     //
     // Cluster Report:
     //
-    server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+    //server = 'http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi';
+    var server = 'http://www.ncbi.nlm.nih.gov/snp/';
+    //url = server + rs_number;
     // snp1-rsum
     rs_number = data.snp1.rsnum.substring(2);
+    console.log(data)
     params = {
         rs : rs_number
     };

LDlink/LDmatrix.py

@@ -205,6 +205,16 @@ def calculate_matrix(snplst, pop, request, web, request_method, genome_build, r2
                 alleles = a1 + "/" + a2
                 allele_lst.append(alleles)
 
+            else:
+                if len(snp_dict) > 1:
+                    output["warning"] = str(output["warning"] if "warning" in output else "")  + rs_input+ " variant is not a biallelic"
+                else:
+                    output["error"] = str(output["error"] if "error" in output else "")  + rs_input+ " variant is not a biallelic"
+                    json_output = json.dumps(output, sort_keys=True, indent=2)
+                    print(json_output, file=out_json)
+                    out_json.close()
+                    return("", "")
+
 
     # Calculate Pairwise LD Statistics
     all_haps = hap1 + hap2

LDlink/LDpop.py

@@ -194,7 +194,7 @@ def calculate_pop(snp1, snp2, pop, r2_d, web, genome_build, request=None):
 
     temp = [snp2, str(snp2_coord['chromosome']), snp2_coord[genome_build_vars[genome_build]['position']]]
     (vcf2, head2, output2) = get_query_variant_c(temp, pop_split, str(request), genome_build, False,output)   
-    if vcf1 == None or vcf2 == None:
+    if vcf1 == None or vcf2 == None or "error" in output:
         #if web:
         output = json.dumps(output, sort_keys=True, indent=2)
         return output

LDlink/index.html

@@ -40,7 +40,7 @@
 	<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/media/css/jquery.dataTables.min.css" integrity="sha256-4vA/Qvj3cRozXbsauVemzsbGBdKSD4GVsVaaMjYTuRk=" crossorigin="anonymous">	
 	<link rel="stylesheet" href="/common/css/style.css">
 	<link rel="stylesheet" href="/common/css/social.css">
-	<link rel="stylesheet" href="LDlink-5.5.1.css">
+	<link rel="stylesheet" href="LDlink-5.5.2.css">
 </head>
 
 <!-- <body class="d-flex flex-column vh-100" role="document"> -->
@@ -2722,7 +2722,7 @@ <h3 class="modal-title apiaccess">Modal title</h3>
 						<pre class="apiaccess-examples">
 							curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop": "CEU","r2_d": "d", "genome_build": "grch37"}' 'https://ldlink.nci.nih.gov/LDlinkRest/ldmatrix?token=faketoken123'
 						</pre>
-						<p><i>Note: POST requests can support up to 1,000 SNPs.</i></p>
+						<p><i>Note: POST requests can support up to 2,500 SNPs.</i></p>
 					</p>
 					<p><a class="help-anchor-link" href="#LDpair">LDpair</a><br>
 						<pre class="apiaccess-examples">
@@ -2890,7 +2890,7 @@ <h4 class="modal-title">Modal title</h4>
 	<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.min.js" integrity="sha256-Sk3nkD6mLTMOF0EOpNtsIry+s1CsaqQC1rVLTAy+0yc=" crossorigin="anonymous"></script>	
 	<script src="https://cdn.jsdelivr.net/npm/[email protected]/build/output/knockout-latest.js" integrity="sha256-TwqMvYd1Dm109PGsukUkZ5vwLfsPCzY0YGG9eBMPBOE=" crossorigin="anonymous"></script>
 	<script src="https://cdn.jsdelivr.net/npm/[email protected]/knockout.mapping.js" integrity="sha256-TUlOKeuoLfKJnB2YhKMgopAf5JurOPSCdfqw0jBlkXw=" crossorigin="anonymous"></script>
-	<script type="text/javascript" src="LDlink-5.5.1.js"></script>
+	<script type="text/javascript" src="LDlink-5.5.2.js"></script>
 	<script type="text/javascript" src="/common/js/purify.js"></script>
 	<script type="text/javascript" src="/common/js/bootstrap-multiselect.js"></script>
 	<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/jquery.browser.min.js" integrity="sha256-Rr2aTI0oGDN2yUVggLBqR2hq8L33245rgO7SdZXj3po=" crossorigin="anonymous"></script>	

LDlink/news-5.5.1.html → LDlink/news-5.5.2.html

@@ -1,3 +1,8 @@
+<p><b>LDlink 5.5.2 Release (3/25/2023)</b></p>
+<ul>
+    <li>Fix the multiallelic error message for LDpair</li>
+</ul>
+<br>
 <p><b>LDlink 5.5.1 Release (11/15/2022)</b></p>
 <ul>
     <li>Add a link to FORGEdb scoring scheme for LDassoc and LDproxy</li>