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interactome-results.php
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="Host-pathogen Interactome Results">
<meta name="author" content="Raghav Kataria">
<!-- App Favicon -->
<link rel="shortcut icon" href="assets/images/gallery/favicon.ico">
<!-- App title -->
<title>Interactome - TRustDB</title>
<!-- Plugins css-->
<link href="assets/plugins/multiselect/css/multi-select.css" rel="stylesheet" type="text/css" />
<!-- DataTables -->
<!-- Custom box css -->
<link href="assets/plugins/custombox/css/custombox.min.css" rel="stylesheet">
<!-- Switchery css -->
<link href="assets/plugins/switchery/switchery.min.css" rel="stylesheet" />
<!-- Bootstrap CSS -->
<link href="assets/css/bootstrap.min.css" rel="stylesheet" type="text/css" />
<!-- App CSS -->
<link href="assets/css/style.css" rel="stylesheet" type="text/css" />
<!-- Modernizr js -->
<script src="assets/js/modernizr.min.js"></script>
<!-- Sigma js -->
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-DCNJT2KP9D"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-DCNJT2KP9D');
</script>
</head>
<?php
header("Access-Control-Allow-Origin: *");
?>
<body>
<!-- Navigation Bar-->
<nav class="navbar navbar-expand-lg navbar-light bg-light">
<div class="container-fluid pl-5">
<div class="row w-100 pl-4">
<div class="col">
<a class="" href="http://127.0.1.1:80">
<img src='assets/images/kaabil_logo.png' height="70" alt="">
</a>
</div>
<div class="col-5">
</div>
<div class="col-auto">
<a href="https://www.usu.edu/"><img src='assets/images/gallery/usu-logo1.png' height="70px"></a>
</div>
</div>
</div>
</nav>
<nav class="container-fluid usu-bg pl-5">
<div class="row py-3 pl-5">
<div class="col-auto pt-2">
<a href="index.html" class="rk-nav-item"><i class="zmdi zmdi-home"></i> Home</a>
</div>
<div class="col-auto pt-2">
<div class="dropdown">
<div class="rk-nav-item dropdown-toggle" type="button" id="dropdownMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<i class="pe-7s-hammer"></i> Tools
</div>
<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" href="interolog-wheat.html">Interactomics</a>
<a class="dropdown-item" href="searchTrustDB.html">Advanced search module</a>
<a class="dropdown-item" href="blast-submittion.html">BLAST search</a>
</div>
</div>
</div>
<div class="col-auto pt-2">
<div class="dropdown">
<div class="rk-nav-item dropdown-toggle" type="button" id="dropdownMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<i class="zmdi zmdi-format-list-bulleted"></i> Features
</div>
<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" href="triticumHPI.php">Host-pathogen interactions</a>
<div class="dropdown-divider"></div>
<h6 class="ml-3" style="color:black"><b>Host</b></h6>
<a class="dropdown-item" href="transcriptionFactors.php">Transcription Factors</a>
<a class="dropdown-item" href="localizationHost.php">Subcellular Localization Annotations</a>
<a class="dropdown-item" href="geneontologyHost.php">Gene Ontology (GO) Term Annotations</a>
<a class="dropdown-item" href="domainsHost.php">Functional Domain Mappings (InterPro)</a>
<hr>
<h6 class="ml-3" style="color:black"><b>Pathogen</b></h6>
<a class="dropdown-item" href="ortholog.php"><i>Puccinia</i> species Orthologs</a>
<a class="dropdown-item" href="localization.php">Subcellular Localization Annotations</a>
<a class="dropdown-item" href="geneontology.php">Gene Ontology (GO) Term Annotations</a>
<a class="dropdown-item" href="domains.php">Functional Domain Mappings (InterPro)</a>
<a class="dropdown-item" href="effector.php">Effector Proteins</a>
<a class="dropdown-item" href="secretory.php">Secretory Proteins</a>
<a class="dropdown-item" href="effectors.php">Effector and Secretory Proteins</a>
</div>
</div>
</div>
<div class="col-auto pt-2">
<a href="genomicInformation.html" class="rk-nav-item"><i class="fa fa-database"></i> Datasets</a>
</div>
<div class="col-auto pt-2">
<a href="help.html" class="rk-nav-item"><i class="ion-document-text"></i> User guide </a>
</div>
<div class="col-auto ml-auto">
<form role="search" class="form-inline text-right">
<select class="form-control select2 mr-2" id="searchSelect">
<optgroup label="Puccinia species [Infecting Triticum]">
<option value="pug99">Puccinia graminis Ug99</option>
<option value="pgt21">Puccinia graminis 21-0</option>
</optgroup>
</select>
<input id="proteinTOsearch" placeholder="Search e.g: 'GMQ_00017T0'" class="form-control mr-2" type="text">
<a id="proteinSender" href=""><i class="fa fa-search" style="color:rgb(38, 92, 194)"></i></a>
</form>
</div>
</div>
</nav>
<!-- End Navigation Bar-->
<!-- ============================================================== -->
<!-- Start right Content here -->
<!-- ============================================================== -->
<div class="wrapper">
<div class="container">
<div class="row">
<div class="col-md-7">
<?php
ini_set('display_errors', 0);
$namer = $_GET['result'];
$running_bool = file_exists('tmp/' . $namer . '_OutputTaskInfo.txt'); ///if exist is running
$finished_bool = file_exists('tmp/' . $namer . '_Output.txt'); ///if exist is finished
$empty_results = true;
if($finished_bool){
$num_interactions = sizeof(file('tmp/' . $namer . '_Output.txt'));
if($num_interactions > 0){
$empty_results = false;
}
if(!($empty_results)){
$filenameInfo = 'tmp/' . $namer . '_OutputTaskInfo.txt';
$fileInfo = fopen($filenameInfo,"r");
$odd = true;
echo "<div class='card m-b-20' style='background-color: #ffdb99; border-color: #333;'>";
echo "<div class='card-body'>";
$lineNumber = 1;
while(! feof($fileInfo)){
$line = fgets($fileInfo);
if($line != false && $line != '\n' && trim($line) != ''){
if($lineNumber==1){
echo "<h5 class='card-title' style='color:#ff3a19;'>".$line."</h5>";
} else if($lineNumber==2){
echo "<h6 style='font-style: italic;' 'color:#ff3a19;'>".$line."</h6>";
} else if($lineNumber==3 || $lineNumber==4 || $lineNumber==5 ){
$separatedLine = explode(";",$line);
if($lineNumber==3 || $lineNumber==4 ){
echo "<b>".$separatedLine[0]."; </b>".$separatedLine[1]."</span>";
} else {
echo "<b>".$separatedLine[0]."; </b>".$separatedLine[1]."</span></br></br>";
}
} else if($lineNumber==6){
echo "<h6 style='font-style: italic;' 'color:#ff3a19;'>".$line."</h6>";
} else if($lineNumber==7 || $lineNumber==8 || $lineNumber==9 ){
$separatedLine = explode(";",$line);
if($lineNumber==7 || $lineNumber==8 ){
echo "<b>".$separatedLine[0]."; </b>".$separatedLine[1]."</span>";
} else {
echo "<b>".$separatedLine[0]."; </b>".$separatedLine[1]."</span></br></br>";
}
} else if($lineNumber==10){
echo "<h6 style='color:#ff3a19;'>".$line."</h6>";
}
}
$lineNumber = $lineNumber +1;
}
// while(! feof($fileInfo)){
// $line = fgets($fileInfo);
// if($line != false && $line != '\n' && trim($line) != ''){
// if($lineNumber==1){
// echo "<h5 class='card-title' style='color:#ff3a19;'>".$line."</h5>";
// } else if($lineNumber==2){
// echo "<h6 style='color:#ff3a19;'>".$line."</h6>";
// } else if($lineNumber==3 || $lineNumber==4 || $lineNumber==5 ){
// $separatedLine = explode(":",$line);
// if($lineNumber==3 || $lineNumber==4 ){
// echo "<b >".$separatedLine[0].":</b><span style='font-style: italic;''>".$separatedLine[1]. "</span> ";
// } else {
// echo "<b >".$separatedLine[0].":</b><span style='font-style: italic;'>".$separatedLine[1]. "</span></br>";
// }
// } else {
// if($lineNumber == 6 || $lineNumber == 10){
// echo "<b style='color:#ff3a19;'>".$line."</b></br>";
// } else {
// $separatedLine = explode(":",$line);
// echo "<b>".$separatedLine[0].":</b>".$separatedLine[1]. "";
// }
// if($lineNumber == 9 || $lineNumber == 13 ){
// echo "</br>";
// }
// }
// }
// $lineNumber = $lineNumber +1;
// }
echo "</div>";
echo "</div>";
echo "</div>";
echo "<div class='col-md-5'>
<button id='seeNetwork' type='button' class='btn btn-block btn-lg btn-info waves-effect waves-light'><i class='ion-network' style='font-size: 195px'></i> Network Visualization</button>";
echo "</div>";
fclose($fileInfo);
}
}
?>
</div>
<div class="card-box">
<?php
if($finished_bool && !($empty_results)){
$namer = $_GET['result'];
$filenameInfo = 'tmp/' . $namer . '_Output.txt';
$num_interactions = sizeof(file($filenameInfo));
if($num_interactions<=10000){
echo ' <table id="datatable-buttons" class="table table-striped table-bordered" cellspacing="0" width="100%">';
echo ' <thead>
<tr role="row">
<th class="sorting_asc" tabindex="0" aria-controls="datatable-buttons" rowspan="1" colspan="1" aria-sort="ascending" aria-label="Host: activate to sort column descending" style="width: 169px;">Host Protein</th>
<th class="sorting" tabindex="0" aria-controls="datatable-buttons" rowspan="1" colspan="1" aria-label="Pathogen: activate to sort column ascending" style="width: 248px;">Pathogen Protein</th>
<th class="sorting" tabindex="0" aria-controls="datatable-buttons" rowspan="1" colspan="1" aria-label="Database: activate to sort column ascending" style="width: 121px;">Database</th>
<th class="sorting" tabindex="0" aria-controls="datatable-buttons" rowspan="1" colspan="1" aria-label="Host organism: activate to sort column ascending" style="width: 121px;">Host Interactor</th>
<th class="sorting" tabindex="0" aria-controls="datatable-buttons" rowspan="1" colspan="1" aria-label="Pathogen organism: activate to sort column ascending" style="width: 121px;">Pathogen Interactor</th>
</tr>
</thead>';
} else {
echo ' <table class="table">';
echo ' <thead>
<tr>
<th>Host</th>
<th>Pathogen</th>
<th>Database</th>
<th>Host Interactor</th>
<th>Pathogen Interactor</th>
</tr>
</thead>';
}
$fileTabular = fopen($filenameInfo,"r");
$odd = true;
include 'dictionary.php';
while(! feof($fileTabular)){
$line = fgets($fileTabular);
if($line != false && $line != '\n' && trim($line) != ''){
$separatedLine = explode("\t",$line);
if($odd){
echo '<tr role="row" class="odd">';
} else {
echo '<tr role="row" class="even">';
}
// echo '<td class="sorting_1"><a href="https://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=' . $separatedLine[2] . '" target="_blank">'. $separatedLine[2] .'</a></td>';
// echo '<td><a href="http://fungi.ensembl.org/Multi/Search/Results?species=all;idx=;q=' . $separatedLine[3] . '" target="_blank">'. $separatedLine[3] .'</a></td>';
echo '<td>' . $separatedLine[2] . '</td>';
echo '<td>' . $separatedLine[3] . '</td>';
echo '<td>' . $separatedLine[4] . '</td>';
///Links to respective PPI databases///
if($separatedLine[4]=="mintdb") {
echo '<td class="sorting_1"><a href="https://www.uniprot.org/uniprot/' . $separatedLine[1] . '" target="_blank">'. $separatedLine[1] .'</a></td>';
echo '<td class="sorting_1"><a href="https://www.uniprot.org/uniprot/' . $separatedLine[0] . '" target="_blank">'. $separatedLine[0] .'</a></td>';
}
if($separatedLine[4]=="hpidb") {
echo '<td class="sorting_1"><a href="https://www.uniprot.org/uniprot/' . $separatedLine[1] . '" target="_blank">'. $separatedLine[1] .'</a></td>';
echo '<td class="sorting_1"><a href="https://www.uniprot.org/uniprot/' . $separatedLine[0] . '" target="_blank">'. $separatedLine[0] .'</a></td>';
}
if($separatedLine[4]=="stringdb") {
echo '<td class="sorting_1"><a href="https://string-db.org/network/' . $separatedLine[1] . '" target="_blank">'. $separatedLine[1] .'</a></td>';
echo '<td class="sorting_1"><a href="https://string-db.org/network/' . $separatedLine[0] . '" target="_blank">'. $separatedLine[0] .'</a></td>';
}
if($separatedLine[4]=="intactdb") {
echo '<td class="sorting_1"><a href="https://www.ebi.ac.uk/intact/imex/main.xhtml?query=' . $separatedLine[1] . '" target="_blank">'. $separatedLine[1] .'</a></td>';
echo '<td class="sorting_1"><a href="https://www.ebi.ac.uk/intact/imex/main.xhtml?query=' . $separatedLine[0] . '" target="_blank">'. $separatedLine[0] .'</a></td>';
}
if($separatedLine[4]=="dipdb") {
echo '<td class="sorting_1"><a href="https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?PK=' . trim(explode("|", $separatedLine[1])[0], "DIP-") . '" target="_blank">'. explode("|", $separatedLine[1])[0] .'</a></td>';
echo '<td class="sorting_1"><a href="https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?PK=' . trim(explode("|", $separatedLine[0])[0], "DIP-") . '" target="_blank">'. explode("|", $separatedLine[0])[0] .'</a></td>';
}
if($separatedLine[4]=="phibasedb") {
echo '<td class="sorting_1"><a href="https://www.uniprot.org/uniprot/' . $separatedLine[1] . '" target="_blank">'. $separatedLine[1] .'</a></td>';
echo '<td class="sorting_1"><a href="https://www.uniprot.org/uniprot/' . $separatedLine[0] . '" target="_blank">'. $separatedLine[0] .'</a></td>';
}
if($separatedLine[4]=="biogriddb") {
echo '<td class="sorting_1"><a href="https://www.ncbi.nlm.nih.gov/search/all/?term=' . $separatedLine[1] . '" target="_blank">'. $separatedLine[1] .'</a></td>';
echo '<td class="sorting_1"><a href="https://www.ncbi.nlm.nih.gov/search/all/?term=' . $separatedLine[0] . '" target="_blank">'. $separatedLine[0] .'</a></td>';
}
echo '</tr>';
}
}
fclose($fileTabular);
} else if($finished_bool && $empty_results){
echo '<h1 style="color: #039cfd;">End of the session.</h1><h2 style="color: #1bb99a;">No successfull Host-Pathogen Interactions were predicted using Interolog method on this dataset, please try other options and resubmit. Thanks.</h2>';
} else if($running_bool){
header("Refresh: 30;");
echo '<h1 style="color: #039cfd;">RUNNING.</h1><h2 style="color: #1bb99a;">This page will refresh in 30 seconds.</h2>';
} else{
header("Refresh: 60;");
echo '<h1 style="color: #039cfd;">QUEUED or INACTIVE.</h1><h2 style="color: #1bb99a;">This page will refresh in 60 seconds.</h2>';
}
?>
</tbody>
</table>
</div>
<!-- end row -->
</div> <!-- container -->
<!-- Footer -->
<footer class="footer">
© 2022  |  <a href="https://www.usu.edu" target="_blank">Utah State University</a>  |  <a href="http://127.0.1.1:80" target="_blank">Kaundal Artificial Intelligence & Advanced Bioinformatics Laboratory</a>  |  <a href="https://www.psc.usu.edu" target="_blank">Department of Plants, Soils, and Climate</a>  |  <a href="https://www.biosystems.usu.edu" target="_blank">Center for Integrated BioSystems </a>
</footer>
<!-- End Footer -->
</div> <!-- End wrapper -->
<!-- jQuery -->
<script src="https://cdn.jsdelivr.net/npm/axios/dist/axios.min.js"></script>
<script src="assets/js/jquery.min.js"></script>
<script src="assets/js/popper.min.js"></script><!-- Tether for Bootstrap -->
<script src="assets/js/bootstrap.min.js"></script>
<script src="assets/js/waves.js"></script>
<script src="assets/js/jquery.nicescroll.js"></script>
<script src="assets/plugins/switchery/switchery.min.js"></script>
<script src="assets/plugins/bootstrap-tagsinput/js/bootstrap-tagsinput.js"></script>
<script type="text/javascript" src="assets/plugins/multiselect/js/jquery.multi-select.js"></script>
<script type="text/javascript" src="assets/plugins/jquery-quicksearch/jquery.quicksearch.js"></script>
<script src="assets/plugins/select2/js/select2.full.min.js" type="text/javascript"></script>
<!-- file uploads js -->
<script src="assets/plugins/fileuploads/js/dropify.min.js"></script>
<!-- Modal-Effect -->
<script src="assets/plugins/custombox/js/custombox.min.js"></script>
<script src="assets/plugins/custombox/js/legacy.min.js"></script>
<!-- App js -->
<script src="assets/js/jquery.core.js"></script>
<script src="assets/js/jquery.app.js"></script>
<!-- Required datatable js -->
<script src="assets/plugins/datatables/jquery.dataTables.min.js"></script>
<script src="assets/plugins/datatables/dataTables.bootstrap4.min.js"></script>
<!-- Buttons examples -->
<script src="assets/plugins/datatables/dataTables.buttons.min.js"></script>
<script src="assets/plugins/datatables/buttons.bootstrap4.min.js"></script>
<script src="assets/plugins/datatables/jszip.min.js"></script>
<script src="assets/plugins/datatables/pdfmake.min.js"></script>
<script src="assets/plugins/datatables/vfs_fonts.js"></script>
<script src="assets/plugins/datatables/buttons.html5.min.js"></script>
<script src="assets/plugins/datatables/buttons.print.min.js"></script>
<script src="assets/js/config.js"></script>
<script type="text/javascript">
$(document).ready(function() {
/*
const email = document.getElementById('email-span').textContent;
const messageBody = window.location.href;
const password = EPASSWORD;
const subjectLine = "TRustDB Interactome Results";
const recipient = email;
const user = 'TRustDB';
const body = {
password,
messageBody,
subjectLine,
recipient,
user
}
axios.post('http://127.0.1.1:80/api/email/send', body)
.then(res => {
console.log(res);
})
.catch(err => {
console.log('Error');
console.log(err);
})
*/
// Buttons examples
var table = $('#datatable-buttons').DataTable({
lengthChange: false,
buttons: ['copy', 'excel', 'pdf']
});
table.buttons().container()
.appendTo('#datatable-buttons_wrapper .col-md-6:eq(0)');
} );
$("#seeNetwork").click(function() {
var resultUrl = "network-interactome.php?result=" + <?php echo(json_encode($namer)); ?>;
window.open(resultUrl);
});
$("#proteinTOsearch").on('input', function() {
var proteinName = $(this).val();
if($.trim(proteinName)!=""){
$('#proteinSender').attr('href', "proteinSearchQuery.php?protein="+$.trim(proteinName)+"&species="+$('select#searchSelect').val());
}
});
$("#searchSelect").change(function() {
$('#proteinSender').attr('href', "proteinSearchQuery.php?protein="+$.trim($('input#proteinTOsearch').val())+"&species="+$(this).val());
});
</script>
</body>
</html>