8/24 commit

Fixed bugs, added features
johnoooh · Aug 24, 2022 · b2a888c · b2a888c
1 parent 5a6d02e
commit b2a888c
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Showing 11 changed files with 547 additions and 26 deletions.
diff --git a/._connection.php b/._connection.php
diff --git a/GenomeDetail.php b/GenomeDetail.php
@@ -143,7 +143,7 @@ class RnaSeqInfo
               //$functiondata.='<div class="row"><table>';
               $domst = $row["Feature_Start"];
               $domed = $row["Feature_End"];
-              $domProtst = ($row["Start"]+$row["Feature_Start"])/3;
+              $domProtst = (intval($row["Start"])+intval($row["Feature_Start"]))/3;
               $domProted = ($row["End"]+$row["Feature_End"])/3;
               array_push($featureArray, array("feature" => $row["domainNameCov2"], "st" => $domst, "end" => $domed, "color" => $colorPaletteId,"AArange" => $row["cov2AAStartEnd"]));
               // $functiondata.='   <tr><td class="col-md-12"><b>'.$row['Feature'].'</b></td></tr>';

diff --git a/GenomeSearch.php b/GenomeSearch.php
@@ -707,7 +707,7 @@ function getGeneDetails(gene, protein) {
 
               var s = document.createElement('script');
               s.type = 'text/javascript';
-              s.src = './JS/domainplotter5.js';
+              s.src = './JS/domainPlotter5.js';
               try {
                 document.body.appendChild(s);
               } catch (e) {

diff --git a/fastas/fastasequences.py b/fastas/fastasequences.py
@@ -0,0 +1,37 @@
+import csv 
+
+genedic=dict()
+orfabli = []
+with open('C:/Users/John/Documents/GitHub/Covid_jorgera/coviddesktop/Covidproj/genestend.csv', newline='') as csvfile:
+    spamreader = csv.reader(csvfile, delimiter=',', quotechar='|')
+    next(spamreader)
+    for sline in spamreader:
+        if (sline[0] != "Non Code" or sline[0] != "ORF10") and sline[0] != ''   :
+            genedic[sline[0]] = [int(sline[3]),int(sline[4]),int(sline[1]),int(sline[2]), int(sline[4])-int(sline[3])]
+        if sline[0].startswith("NSP"):
+            orfabli.append(sline[0])
+
+print(genedic)
+refseq=""
+with open(r"C:\xampp\htdocs\php_su\fastas\reference.fasta","r") as fasta:
+    for line in fasta:
+        if line.startswith(">"):
+            pass
+        else: 
+            refseq+= line.strip()
+
+print(refseq)
+
+
+for item in genedic:
+    genedic[item].append(refseq[genedic[item][0]-1:genedic[item][1]])
+
+print(genedic)
+
+with open("ntseqtable.csv","w") as tabl:
+    string= ""
+    for item in genedic:
+        string+=item
+        string+=","
+        string+= genedic[item][5]
+        string+= ",\n"
diff --git a/fastas/genestend.csv b/fastas/genestend.csv
@@ -0,0 +1,38 @@
+Gene,Start aa,End aa,Start Nt,End Nt,TRSB
+Lead region pre ORF1a & ORF1ab,1,88,1,265,0
+NSP1,89,268,266,805,0
+NSP2,269,906,806,2719,0
+NSP3,907,2851,2720,8554,0
+NSP4,2852,3351,8555,10054,0
+NSP5,3352,3657,10055,10972,0
+NSP6,3658,3947,10973,11842,0
+NSP7,3948,4030,11843,12091,0
+NSP8,4031,4228,12092,12685,0
+NSP9,4229,4341,12686,13024,0
+NSP10,4342,4480,13025,13441,0
+NSP11,4481,4493,13442,13480,0
+NSP12,4481,5412,13442,16236,0
+NSP13,5412,6013,16237,18039,0
+NSP14,6013,6540,18040,19620,0
+NSP15,6540,6886,19621,20658,0
+NSP16,6886,7184,20659,21552,0
+Non Code,7184,7187,21553,21562,0
+Spike,7188,8461,21563,25384,21555
+Non Code,8462,8464,25385,25392,0
+ORF3a,8464,8740,25393,26220,25384
+Non Code,8740,8748,26221,26244,0
+E,8748,8824,26245,26472,26236
+Non Code,8824,8841,26473,26522,0
+M,8842,9064,26523,27191,26472
+Non Code,9064,9067,27192,27201,0
+ORF6,9067,9129,27202,27387,27040
+Non Code,9129,9131,27388,27393,0
+ORF7a,9131,9253,27394,27759,27388
+ORF7b,9252,9296,27756,27887,0
+Non Code,9296,9298,27888,27893,0
+ORF8,9298,9420,27894,28259,27887
+Non Code,9420,9424,28260,28273,0
+N,9425,9844,28274,29533,28259
+Non Code,9845,9852,29534,29557,0
+ORF10,9853,9891,29558,29674,0
+End Region,9892,9968,29675,29903,0
diff --git a/fastas/reference.fasta b/fastas/reference.fasta
diff --git a/fastas/reference.js b/fastas/reference.js
diff --git a/fastas/reference.php b/fastas/reference.php
@@ -0,0 +1,22 @@
+!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>tatDB Page</title>
+    <link href="bootstrap.css" rel="stylesheet" />
+    <link rel="stylesheet" type="text/css" href="style.css" />
+    <link rel="stylesheet" type="text/css" href="front.css" />
+    <div class="panel-group">
+        <nav class="navbar navbar-default">
+            <div class="container-fluid">
+                <div class="navbar-header">
+                  <a class="navbar-brand" href="index.php">tatDB</a>
+                </div>
+                <ul class="nav navbar-nav">
+                    <li><a href="index.php">Home</a></li>
+                    <li><a href="search.php">Search</a></li>
+                    <li class="active"><a href="reference.php">Reference</a></li>
+                    <li><a href="help.php">Help</a></li>
+                </ul>
+            </div>
+        </nav>
+    </div>
diff --git a/helpimages/weclomepage.png b/helpimages/weclomepage.png
diff --git a/helpimages/welcomedropdown.png b/helpimages/welcomedropdown.png
diff --git a/motifvisualizer.php b/motifvisualizer.php
@@ -216,7 +216,6 @@ function containsAny(str) {
       const nonNTalphabet = ["B","D","E","F","H","I","J","K","L","M","N","O","P","Q","R","S","U","V","W","X","Y","Z",""];
 
     function resetForm(){
-      // console.log("clicked");
       container.innerHTML = '';
       var highlights = document.getElementsByClassName("highlight");
       var parentNode = document.getElementById("repeatDisplay");
@@ -230,28 +229,15 @@ function resetForm(){
       function makeTable(coordarray,substrarray) {
       var repeat = document.getElementById("motif").value;
 
-      // console.log(coordarray);
-      // console.log(substrarray);
       var theTable = document.createElement('table');
-      // theTable.classList.add("table table-bordered");
-      // console.log(typeof(array[1]));
       var coordarray = coordarray.map(function (x) { 
         return parseInt(x, 10); 
         });
 
-      // console.log(typeof(array[1]));
-
-      // coordarray.sort(function(a, b){return a-b});
-      // console.log(coordarray);
-      // console.log(substrarray);
-
       const zip = (a, b) => Array(Math.max(b.length, a.length)).fill().map((_,i) => [a[i], b[i]]);
 
       var zippedArray = zip(coordarray,substrarray);
-      // coordarray.sort(function(a, b){return a-b});
-      // console.log(zippedArray[0][0]);
       zippedArray.sort(function(x,y){return x[0] - y[0];});
-      // console.log(zippedArray);
 
 
       var arrayLength = zippedArray.length;
@@ -319,7 +305,7 @@ function makeHTMLtable(data){
       var parsedData = JSON.parse(data);
       // console.log("in makehtmltable");
       // console.log(parsedData[0]);
-      console.log(parsedData[0].proteins);
+      // console.log(parsedData[0].proteins);
       // console.log(parsedData[0].substrings.length);
       plotrepeats(parsedData[0].coordinates);
 
@@ -349,8 +335,15 @@ function makeHTMLtable(data){
         tdsuper.classList.add("comp-table-row-td");
 
         var superText = document.createElement("a");
+        var superLink = document.createTextNode(parsedData[0].substrings[i]);
+        superText.appendChild(superLink);
+        superText.href = 'motifvisualizer.php?repeat='+parsedData[0].substrings[i];
         superText.innerText = parsedData[0].substrings[i];
-        superText.addEventListener("click",superStringSet);
+
+
+        // console.log("here!!!!!!!!!!!!!!!!!!!");
+        // console.log(parsedData[0].substrings[i]);
+        // superText.addEventListener("click",superStringSet);
         tdsuper.appendChild(superText);
 
         theTable.appendChild(tdsuper);
@@ -362,13 +355,19 @@ function makeHTMLtable(data){
     function superStringSet(){
       // console.log(this.innerText);
       document.getElementById("motif").value = this.innerText;
+
       getRepeatData();
     }
 
 
     function getRepeatData() {
 
-
+      if (previousRepeats){
+        previousRepeats.push(document.getElementById("motif").value)
+      }else{
+        var previousRepeats=[document.getElementById("motif").value]
+      }
+
       resetForm()
 
       // container.innerHTML = '';
@@ -386,12 +385,7 @@ function getRepeatData() {
       var xmlhttp = new XMLHttpRequest();
       xmlhttp.onreadystatechange = function() {
           if (this.readyState == 4 && this.status == 200) {   
-          // console.log(this.responseText);
-          // console.log(this);
 
-          // var parsedData = JSON.parse(this.responseText);
-          // console.log(this.responseText);
-          // console.log(typeof(this.responseText));
           makeHTMLtable(this.responseText);
 
 
@@ -404,10 +398,9 @@ function getRepeatData() {
 
     window.onload = function() {
       if (<?php echo $repeatExternal; ?>  == 1){
-        console.log("test");
         getRepeatData();
+
       }else{
-        console.log("test");
         getRepeatData();
       }