adjust pmid position;add release news

CBIIT · Aug 3, 2023 · 28d128d · 28d128d
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commit 28d128d
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Showing 4 changed files with 12 additions and 6 deletions.
diff --git a/client/index.html b/client/index.html
@@ -32,7 +32,7 @@
 	<link rel="stylesheet" href="lib/[email protected]/jquery.dataTables.min.css">	
 	<link rel="stylesheet" href="css/style.css">
 	<link rel="stylesheet" href="css/social.css">
-	<link rel="stylesheet" href="LDlink.css?v=5.6.4">
+	<link rel="stylesheet" href="LDlink.css?v=5.6.5">
 </head>
 
 <!-- <body class="d-flex flex-column vh-100" role="document"> -->
@@ -2112,8 +2112,8 @@ <h3>Proxy Variants</h3>
 									<thead title="Shift-click column headers to sort by multiple levels">
 										<tr>
 											<!-- <th class="dt-head-left dt-body-left">Query RS Number</th> -->
-											<th class="dt-head-left dt-body-left">PMID</th>
 											<th class="dt-head-left dt-body-left">GWAS Trait</th>
+											<th class="dt-head-left dt-body-left">PMID</th>
 											<th class="dt-head-left dt-body-left">RS Number</th>
 											<th class="dt-head-left dt-body-left">Position (<span class="ldtrait-position-genome-build-header">GRCh37</span>)</th>
 											<th class="dt-head-left dt-body-left">Alleles</th>
@@ -2911,7 +2911,7 @@ <h4 class="modal-title">Modal title</h4>
 	<script src="lib/[email protected]/jquery.dataTables.js"></script>
 	<script src="lib/[email protected]/html2canvas.min.js"></script>
 	<script src="https://maps.googleapis.com/maps/api/js?key=@gmap_key@"></script>
-	<script src="LDlink.js?v=5.6.4"></script>
+	<script src="LDlink.js?v=5.6.5"></script>
 	<script>_satellite.pageBottom();</script>
 </body>
 

diff --git a/client/news.html b/client/news.html
@@ -1,3 +1,9 @@
+<p><b>LDlink 5.6.5 Release (8/6/2023)</b></p>
+<ul>
+    <li>Added more citations for LDtrait and LDexpress</li>
+    <li>Added PUBMEDID(PMID) for LDtrait outputs</li>
+</ul>
+<br>
 <p><b>LDlink 5.6.4 Release (7/6/2023)</b></p>
 <ul>
     <li>Replaced CDN-hosted assets</li>

diff --git a/server/LDlink.py b/server/LDlink.py
@@ -1406,7 +1406,7 @@ def ldtrait():
                     trait["error"] = json_dict["error"]
                 else:
                     with open(tmp_dir + 'trait_variants_annotated' + reference + '.txt', 'w') as f:
-                        f.write("Query\tPMID\tGWAS Trait\tRS Number\tPosition (" + genome_build_vars[genome_build]['title'] + ")\tAlleles\tR2\tD'\tRisk Allele\tEffect Size (95% CI)\tBeta or OR\tP-value\n")
+                        f.write("Query\tGWAS Trait\tPMID\tRS Number\tPosition (" + genome_build_vars[genome_build]['title'] + ")\tAlleles\tR2\tD'\tRisk Allele\tEffect Size (95% CI)\tBeta or OR\tP-value\n")
                         for snp in thinned_snps:
                             for matched_gwas in details[snp]["aaData"]:
                                 f.write(snp + "\t")

diff --git a/server/LDtrait.py b/server/LDtrait.py
@@ -109,10 +109,10 @@ def get_gwas_fields(query_snp, query_snp_chr, query_snp_pos, found, pops, pop_id
                 matched_record = []
                 # Query SNP
                 # matched_record.append(query_snp)
-                # GWAS Trait
+                matched_record.append(record["DISEASE/TRAIT"]) 
+                  # GWAS Trait
                 # add PMID on Jul 19 2023 
                 matched_record.append(record["PUBMEDID"]) 
-                matched_record.append(record["DISEASE/TRAIT"]) 
                 # RS Number
                 matched_record.append("rs" + record["SNP_ID_CURRENT"]) 
                 # Position