limit variants to 500 in pgs

sdk/get23.js

@@ -254,7 +254,7 @@ get23.userTxtsByPhenotypeId = async function (phenoId, keysLen, maxKeys) {
     if (combined.length < maxUsers) {
         cleanUsers =  get23.usersByFileType("23andme", combined)
     } else {
-        cleanUsers = await (get23.usersByFileType("23andme", combined.slice(7, 15)))//.slice(0,maxUsers)
+        cleanUsers = await (get23.usersByFileType("23andme", combined.slice(7, 19)))//.slice(0,maxUsers)
         //console.log("Warning: user txts for phenotypeID", phenoId, "> 7. First 6 files used.")
         console.log("cleanUsers",cleanUsers)
     }

sdk/getPgs.js

@@ -79,7 +79,7 @@ const timeout = (ms) => {
 getPgs.scoreFiles = async function(pgsIds) {
 
     // var scores = await scoreFilesTable.getItem("scoreFiles")
-    let scores = storage.saveData(scoreFilesTable,`https://www.pgscatalog.org/rest/score/`,pgsIds)
+    let scores = storage.saveData(scoreFilesTable,`https://www.pgscatalog.org/rest/score/`,[pgsIds])
     return scores
 }
 
@@ -99,6 +99,7 @@ getPgs.traitsData = async function(traits) {
         storeName: "traitsData"
     })
     let dt
+    let traitFiles = getPgs.traitFiles()
     if ((await traitsData.getItem("traitsData")) === null) {
 
         dt = traits.map(trait => {
@@ -131,18 +132,24 @@ getPgs.traitsData = async function(traits) {
 }
 
 //console.log("pgs",await getscoreFiles(["PGS002130"]))
-
+// get pgs text file filtered by variants number
 getPgs.loadScoreHm = async function(entry, build = 37, range) {
-    let txt = ""
+    const scoreFiles = await getPgs.scoreFiles(entry)
+    console.log("entry, scoreFiles",entry, scoreFiles)
+    const variants_number = scoreFiles[0].variants_number
+    console.log("variants_number",variants_number)
+
+    let txt
     let dt
     dt = await pgsTxts.getItem(entry); // check for users in localstorage
+    if(variants_number<500){
+        // console.log("variants_number<500",variants_number)
     if (entry == null){
-         txt = "no pgs entry provided"
-        return txt
+        console.log("no pgs entry provided")
+        // return txt
     } else if (dt == null){
         console.log("PGS entry: ",entry," PGS txt file not found in storage",dt)
 
-        txt = ""
         entry = "PGS000000".slice(0, -entry.length) + entry
         // https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/Harmonized/PGS000004_hmPOS_GRCh37.txt.gz
         const url = `https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/${entry}/ScoringFiles/Harmonized/${entry}_hmPOS_GRCh${build}.txt.gz` //
@@ -169,17 +176,22 @@ getPgs.loadScoreHm = async function(entry, build = 37, range) {
         if (response?.ok) {
             ////console.log('Use the response here!');
         } else {
-            txt = `:( Error loading PGS file. HTTP Response Code: ${response?.status}`
+            // txt = `:( Error loading PGS file. HTTP Response Code: ${response?.status}`
+            console.log(':( Error loading PGS file. HTTP Response Code: ${response?.status}')
             document.getElementById('pgsTextArea').value = txt
         }
         txt = await getPgs.parsePGS(entry, txt)
         pgsTxts.setItem(entry, txt)
-} else if (dt != null){
-    console.log("pgs txt file for",entry,"found in storage")
-    txt = dt
+
+    } else if (dt != null){
+        console.log("pgs txt file for",entry,"found in storage",dt)
+        txt = dt
+    }else{ 
+        console.log(`pgs file too large: ${variants_number} variants`)
     }
 
-    return txt
+}
+return txt
 }
 
 // create PGS obj and data --------------------------

sdk/prs.js

@@ -105,7 +105,6 @@ PRS.Match2 = function (data) {
         data2.QC = true
         data2.QCtext = ''
     }
-
     return data2
 }
 
@@ -114,15 +113,14 @@ PRS.Match2 = function (data) {
 PRS.calc = async function (matrix) {
     console.log("------------------------")
     console.log("Calculating PRS scores!")
-    console.log("matrix input data 2:", matrix)
-
     let arr = []
     const badIds = []
     // todo remove qc from match2 function
     // todo remove users with old chips
     for (let i = 0; i < matrix.users.txts.length; i++) {
         console.log("---------------------------")
         console.log("processing user #...", i)
+        console.log("matrix", matrix)
 
         for (let j = 0; j < matrix.pgs.txts.length; j++) {
 

sdk/ui.js

@@ -134,16 +134,17 @@ const ui = async function (targetDiv) {
         dt.pgs = {}
         const category = document.getElementById("pgsSelect").value
         console.log("PGS category selected: ", e.target.value)
-        // TODO filter ids by variant number using get scoreFIles
-        let pgsIds = (await (getPgs.idsFromCategory(category))).sort().slice(5, 8)
+        // TODO slice the pgs entries that are <500
+        let pgsIds = (await (getPgs.idsFromCategory(category))).sort().slice(5, 12)
 
         console.log("pgsIds", pgsIds)
-        let pgsTxts = await Promise.all(pgsIds.map(async x => {
+        let pgsTxts = (await Promise.all(pgsIds.map(async x => {
             let res = await getPgs.loadScoreHm(x)
             return res
-        }))
+        }))).filter(item => item);
+        console.log("pgsTxts", pgsTxts)
+
         dt.pgs.category = category
-        dt.pgs.ids = pgsIds
         dt.pgs.txts = pgsTxts
 
         //calculate prs    
@@ -191,7 +192,7 @@ const ui = async function (targetDiv) {
                 x: traces[x].map(x => {
                     let monthDay = x.users.meta.split(/\r?\n|\r|\n/g)[0].slice(-20, -14)
                     let year = x.users.meta.split(/\r?\n|\r|\n/g)[0].slice(-4)
-                    let xlabel = x.users.openSnp.variation +" , name: " + x.users.openSnp.name + " , Date: "  + monthDay +" "+ year
+                    let xlabel = x.users.openSnp.variation +", name: " + x.users.openSnp.name + " , Date: "  + monthDay +" "+ year
                     return xlabel
                 }),
                 mode: 'lines+markers',