user 23andme with new chips

episphere · Apr 5, 2024 · 307a829 · 307a829
1 parent 959aebc
commit 307a829
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Showing 6 changed files with 293 additions and 83 deletions.
diff --git a/index.html b/index.html
@@ -72,11 +72,12 @@ <h4 class="hero_title">Diseasome</h3>
     <div class="tab">
         <button class="tablinks" onclick="openCity(event, 'PGS catalog')">PGS catalog</button>
         <button class="tablinks" onclick="openCity(event, 'OpenSNP')">OpenSNP</button>
-        <button class="tablinks" onclick="openCity(event, 'PRS')">PRS</button>
+        <button id = "prsButton" class="tablinks" onclick="openCity(event, 'PRS')">PRS</button>
     </div>
+<div id = "selection"></div>
 
 
-    <!-- PRS -->
+    <!-- PRS ------------------------------------------>
 
 
     <div id="PRS" class="tabcontent">
@@ -91,9 +92,15 @@ <h3>PRS</h3>
             personal devices, including smartphones, establishing the feasibility of privately calculating personal risk
             scores with up to a few thousand reference genetic variations and from the full 23andMe SNP data file
             (compressed or not).</p>
+
+            <div id=prsDiv>prsDiv</div>
+
+
     </div>
 
-    <!-- 23 and me -->
+
+
+    <!-- 23 and me ------------------------------------------>
 
     <div id="OpenSNP" class="tabcontent">
         <h3>OpenSNP</h3>
@@ -161,15 +168,12 @@ <h6 id="pieHeader"></h6>
         </div>
         <!--  --------------------->
         <div id="Traits" class="tabcontent">
-            <h6 style="color: rgb(6, 137, 231);">Or select a PGS trait below:</h6>
+            <h6 style="color: rgb(6, 137, 231);">Select a PGS trait below:</h6>
         <div id="topBarTraits"></div>
         <div class="spinner-border m-5" style="display: none;" role="status" id="spinner3">
             <span class="visually-hidden">Loading...</span>
         </div>
         <div id="secondBarTraits"></div>
-        <!-- 
-    <div class='graph-container'>
-    </div> -->
         <div id="secondBarTraitsButton"></div>
 
         <div id="betassecondBarTraitsButton"></div>
@@ -178,6 +182,7 @@ <h6 style="color: rgb(6, 137, 231);">Or select a PGS trait below:</h6>
     </div>
     <!-- scripts----------------------------------------------->
     <script src="tabs.js"></script>
+    <script type="module" src="sdk/prs.js"></script>
 
     <script type="module" src="sdk/sdk.js"></script>
     <script type="module" src="sdk/main.js"></script>

diff --git a/sdk/main.js b/sdk/main.js
@@ -70,6 +70,7 @@ functions.get23 = async function(urls) {
     let arr23Txts = []
     for (let i = 0; i < urls.length; i++) {
         let user = await openSnpDbUsers.getItem(urls[i]);
+        console.log(i)
 
         if (user == null) {
             let url2 = 'https://corsproxy.io/?' + urls[i]
@@ -78,14 +79,40 @@ functions.get23 = async function(urls) {
         }
         if (user.substring(0, 37) == '# This data file generated by 23andMe') {
             //console.log("This is a valid 23andMe file:", user.substring(0, 37))
-            let parsedUser = await parse23(user, urls[i])
+            let parsedUser = await functions.parse23(user, urls[i])
             arr23Txts.push(parsedUser)
         } else {
             console.log("ERROR:This is NOT a valid 23andMe file:", user.substring(0, 37))
         }
     }
+    console.log("arr23Txts",arr23Txts)
     return arr23Txts
 }
+
+// create 23andme obj and data --------------------------
+functions.parse23 = async function (txt, url) {
+    // normally info is the file name
+    let obj = {}
+    let rows = txt.split(/[\r\n]+/g)
+    obj.txt = txt
+    obj.url = url
+
+    let n = rows.filter(r => (r[0] == '#')).length
+    obj.meta = rows.slice(0, n - 1).join('\r\n')
+    obj.cols = rows[n - 1].slice(2).split(/\t/)
+    obj.dt = rows.slice(n)
+    obj.dt = obj.dt.map((r, i) => {
+        r = r.split('\t')
+        r[2] = parseInt(r[2])
+        // position in the chr
+        r[4] = i
+        return r
+    })
+    return obj
+}
+
+
+
 // FUNCTIONS------------------------------------------------------------------------
  functions.downloadBlob = function(content, filename, contentType) {
     // Create a blob
@@ -201,7 +228,7 @@ functions.traitsData = async function(traits) {
     return dt
 }
 //--------------------------------------
-functions.getAllPgsIdsByCategory = function(trait) {
+functions.getAllPgsIdsByCategory = async function(trait) {
     let traitFilesArr = []
     let pgsIds = []
     // get trait files that match selected trait from drop down