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proteinSearch.php
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proteinSearch.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="Protein description">
<meta name="author" content="Raghav Kataria">
<!-- App Favicon -->
<link rel="shortcut icon" href="assets/images/gallery/favicon.ico">
<!-- App title -->
<title>TRustDB- Protein search</title>
<!-- 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>
<style type="text/css">
p.closeCategory {
margin-bottom:2px;
}
</style>
<!-- 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>
<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="https://bioinfo.usu.edu">
<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>
<?php
// Start the session
//header("Access-Control-Allow-Origin: *");
ini_set('display_errors',0);
$accession = $_GET['protein'];
$species = $_GET['species'];
include 'dictionary.php';
$outfile = "tmp/".$accession."_".$species.".txt";
$fasta = "tmp/".$accession."_".$species.".fasta";
?>
<!-- End Navigation Bar-->
<!-- ==============================================================
<!-- Start right Content here -->
<!-- ============================================================== -->
<div class="wrapper">
<div class="container" style="width: 75%; padding-top: 20px;">
<!-- Page-Title -->
<?php
$DOMFound = array();
$ISFound = array();
if(file_exists($outfile)){
echo '<div class="row">';
echo ' <div class="col-xs-12 col-lg-12 col-xl-7">';
echo ' <div id="basicPanel" class="card m-b-20 card-body" style="height:460px;">';
$fileTabular = fopen($outfile,"r");
$line = fgets($fileTabular);
echo ' <h5 style=" color: #008000;">'.$line.'</h5>';
echo '<hr>';
$strain = fgets($fileTabular);
echo ' <h6>Strain: </h6><i>'.$speciesDictionary[trim($strain)].'</i>';
echo '<hr>';
echo '<br>';
$description = fgets($fileTabular);
$replicon = fgets($fileTabular);
$repliconAcc = fgets($fileTabular);
$locus_new = fgets($fileTabular);
$genomicRange = fgets($fileTabular);
$length = fgets($fileTabular);
$geneName = fgets($fileTabular);
$oldlocus = fgets($fileTabular);
$HPIFound = array();
$SEFound = array();
$SLFound = "";
$HLBFound = array();
$PSEFound = array();
$annot = array();
while(! feof($fileTabular)){
$line = fgets($fileTabular);
if(substr($line, 0,4)=="HPI:"){
array_push($HPIFound, $line);
} elseif(substr($line, 0,3)=="SE\t"){
array_push($SEFound, $line);
} elseif(substr($line, 0,3)=="SL:"){
$lineExploded = explode(":",$line);
$SLFound = $lineExploded[1];
} elseif(substr($line, 0,3)=="IS\t"){
$lineExploded = explode("\t",$line);
$domLine = $lineExploded[1];
$domLineExploded = explode("_",$domLine);
if(!in_array($lineExploded[1],$DOMFound) & !empty(trim($domLineExploded[1]))){
array_push($DOMFound, $lineExploded[1]);
}
$goTerms = explode("|",$lineExploded[2]);
foreach ($goTerms as &$value){
if(!in_array($value,$GOFound) & trim($value) != ""){
array_push($GOFound, $value);
}
}
if(!in_array($lineExploded[3],$ISFound) & !empty(trim($lineExploded[3]))){
array_push($ISFound, $lineExploded[3]);
}
} elseif(substr($line, 0,4)=="HLB\t"){
$lineExploded = explode("\t",$line);
array_push($HLBFound, $line);
array_push($annot, $lineExploded[1]);
} elseif(substr($line, 0,4)=="PSE:"){
array_push($PSEFound, $line);
}
}
echo '<div class="row">';
echo '<div class="col-md-5">';
echo ' <h6>Description: </h6><p>'.$description.'</p>';
// echo ' <h6>Location: </h6><p>'.$SLFound.'</p>';
// echo ' <h6>Replicon: </h6><p>'.$replicon.'</p>';
echo ' <h6>NCBI Reference Sequence: </h6><p><a href="https://www.ncbi.nlm.nih.gov/nuccore/'.$repliconAcc.'?report=graph" target="_blank"> '.$repliconAcc.'</a></p>';
echo '</div>';
echo '<div class="col-md-5">';
echo ' <h6>Position in replicon (bp): </h6><p>'.$genomicRange.'</p>';
echo ' <h6>Length: </h6><p>'.$length.'</p>';
echo ' <h6>Locus tag: </h6><p>'.$locus_new.'</p>';
echo '</div>';
echo '</div>';
echo '<hr>';
echo ' </div>';
echo ' </div><!-- end col-->';
echo ' <div class="col-xs-12 col-lg-12 col-xl-5">';
echo ' <div id="annotPanel" class="card m-b-20 card-body" style="height:400px; overflow-y:scroll;">';
echo '<hr>';
// echo ' <h6>Subcellular localization: </h6>';
// if(strlen($SLFound) > 0){
// echo ' <p class="closeCategory">'.$SLFound.'</p>';
// }
// echo '<hr>';
echo ' <h6> <b>InterProScan:</b> </h6>';
echo '<hr>';
echo ' <h6> Annotations </h6>';
if(count($ISFound) > 0){
foreach ($ISFound as &$value){
$interproRecord = explode("_",$value);
if(!empty(trim($interproRecord[0]))){
echo ' <p class="closeCategory"><a href="https://www.ebi.ac.uk/interpro/entry/InterPro/'.$interproRecord[0].'/" target="_blank">'. $interproRecord[0] .'</a>: '.$interproRecord[1].'</p>';
}
}
}
echo '<hr>';
echo ' <h6> Functional domains </h6>';
if(count($DOMFound) > 0){
foreach ($DOMFound as &$value){
$domainRecord = explode("_",$value);
if(!empty(trim($domainRecord[1]))){
echo ' <p class="closeCategory">'. $domainRecord[0] .': '.$domainRecord[1].'</p>';
}
}
}
echo '<hr>';
echo ' <h6> Gene Ontology </h6>';
if(count($GOFound) > 0){
echo ' <p class="closeCategory">';
foreach ($GOFound as &$value){
$goRecord = explode("_",$value);
if(!empty(trim($goRecord[0]))){
echo '<a href="http://amigo.geneontology.org/amigo/term/'.$goRecord[0].'" target="_blank">'. $goRecord[0].'</a> ';
}
}
echo '</p>';
}
echo '<hr>';
echo ' </div>';
echo ' </div><!-- end col-->';
echo '</div>';
$furtherAnnot = count($SEFound) + count($HLBFound) + count($HPIFound);
if($furtherAnnot > 0 ){
echo ' <div class="card m-b-20 card-body">';
if(count($SEFound) > 0){
echo '<hr>';
foreach ($SEFound as &$value){
$SERecord = explode("\t",$value);
if(!in_array($SERecord[1],$annot)){
if(!empty(trim($SERecord[1]))){
$pmids = $SERecord[2];
$pmidArray = explode(", ", $pmids);
$pmidString = "";
foreach ($pmidArray as &$valuePMC){
$pmidString = $pmidString.'<a href="https://www.ncbi.nlm.nih.gov/pubmed/'.trim($valuePMC).'" target="_blank">'.trim($valuePMC).'</a>, ';
}
$pmidString = substr($pmidString,0,strlen($pmidString)-2);
echo ' <p>'. $SERecord[1] .' ('.$pmidString.') </p>';
}
}
}
}
if(count($HLBFound) > 0){
echo '<hr>';
foreach ($HLBFound as &$value){
$HLBRecord = explode("\t",$value);
if(!empty(trim($HLBRecord[1]))){
$pmids = $HLBRecord[2];
$pmidString = "";
if(!strpos($pmids,"http")){
$pmidArray = explode(", ", $pmids);
foreach ($pmidArray as &$valuePMC){
$pmidString = $pmidString.'<a href="https://www.ncbi.nlm.nih.gov/pubmed/'.trim($valuePMC).'" target="_blank">'.trim($valuePMC).'</a>, ';
}
$pmidString = substr($pmidString,0,strlen($pmidString)-2);
} else {
$pmidString = '<a href="'.$pmids.'" target="_blank">Link to reference</a>';
}
echo ' <p>'. $HLBRecord[1] .' ('.$pmidString.') </p>';
}
}
}
if(count($HPIFound) > 0){
echo '<hr>';
echo ' <h6>Host-pathogen interactions: </h6>';
foreach ($HPIFound as &$value){
$hpiRecord = explode(":",$value);
if(!empty(trim($hpiRecord[3]))){
$pmids = $hpiRecord[2];
$pmidString = "";
if($pmids != 'Manuscript in preparation'){
$pmidArray = explode(", ", $pmids);
foreach ($pmidArray as &$valuePMC){
$pmidString = $pmidString.'<a href="https://www.ncbi.nlm.nih.gov/pubmed/'.trim($valuePMC).'" target="_blank">'.trim($valuePMC).'</a>, ';
}
$pmidString = substr($pmidString,0,strlen($pmidString)-2);
} else {
$pmidString = 'Predicted with <a href="https://bioinfo.usu.edu/PredHPI/" target="_blank">PredHPI</a>';
}
echo ' <p class="closeCategory">'.$hpiRecord[3].' ('.$pmidString.')</p>';
}
}
}
echo '<hr>';
echo '</div>';
}
echo ' <div class="card m-b-20 card-body">';
echo ' <h5 style=" color: #008000;">Sequence</h5>';
echo '<hr>';
$fastaFile = fopen($fasta,"r");
$line = fgets($fastaFile);
echo $line;
echo '<br>';
$sequence = '';
while(! feof($fastaFile)){
$line = fgets($fastaFile);
$sequence = $sequence.trim($line);
}
echo $sequence;
echo '</div>';
} else {
echo ' <div class="card m-b-20 card-body" style="margin-top:100px;">';
echo '<h1 style="color: #039cfd;">ACCESSION NOT FOUND.</h1><h2 style="color: #1bb99a;">No record was found in TRustDB that matched your query, please retry with another accession. Thanks.</h2>';
echo '</div>';
}
?>
<!-- end row -->
</div>
<!-- end row -->
</div> <!-- container -->
<!-- Footer -->
<footer class="footer">
© 2022  |  <a href="https://www.usu.edu" target="_blank">Utah State University</a>  |  <a href="https://bioinfo.usu.edu" 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="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>
<!-- Counter Up -->
<!-- App js -->
<script src="assets/js/jquery.core.js"></script>
<script src="assets/js/jquery.app.js"></script>
<?php
$countAnnot = count($ISFound) + count($DOMFound);
?>
<script type="text/javascript">
$(document).ready(function(){
var countAnnot = <?php echo(json_encode($countAnnot)); ?>;
console.log(countAnnot);
if(countAnnot==0){
} else if(countAnnot > 0 & countAnnot <= 6){
document.getElementById("basicPanel").style.height = "460px";
document.getElementById("annotPanel").style.height = "460px";
} else if(countAnnot <= 9){
document.getElementById("basicPanel").style.height = "550px";
document.getElementById("annotPanel").style.height = "550px";
} else if(countAnnot <= 18){
document.getElementById("basicPanel").style.height = "650px";
document.getElementById("annotPanel").style.height = "650px";
} else {
document.getElementById("basicPanel").style.height = "800px";
document.getElementById("annotPanel").style.height = "800px";
}
});
</script>
<script>
$("#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>