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search.php
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search.php
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<!-- update 180522 sorting with respect to validated miRTarBase evidence -->
<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<link href="./index_files/base.css" type="text/css" rel="stylesheet">
<link rel="stylesheet" href="https://www.w3schools.com/w3css/4/w3.css">
<title>BiMiR - Search Results</title>
<!--<link href="./index_files/base.css" type="text/css" rel="stylesheet"> -->
<style>
.comment {
width: auto;
margin: 0 auto;
}
a.morelink {
outline: none;
color: #0000ff !important;
}
.morecontent span {
display: none;
}
.inline {
display: inline;
}
.link-button {
background: none;
border: none;
color: blue;
text-decoration: underline;
cursor: pointer;
font-size: 1em;
font-family: serif;
}
.link-button:focus {
outline: none;
}
.link-button:active {
color:red;
}
</style>
<style>
.footer {
position: fixed;
left: 0;
bottom: 0;
width: 100%;
background-color: white;
color: white;
text-align: left;
}
</style>
<script>
function goBack() {
window.history.back();
}
</script>
<!--<script src="./jquery-3.1.1.js"></script> -->
<script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
<script src="readmore.js"></script>
</head>
<body bgcolor="#ffffff" height="100%" width="100%" link="#000000" vlink="#000000" alink="#000000">
<div class="header">
<table border="0" width="100%" style="border-spacing:0;" >
<tbody>
<tr valign="top" colspan="5" style="background-color:rgb(0, 0, 0);">
<td height="20"> </td>
</tr>
<tr valign="top" colspan="4" style="background-color:rgb(3, 45, 67);">
<th align='left' valign='middle' width="100%" colspan="100%" style="font-family:caribri;font-size:120%;font-weight:bold;color:#ffffff;background-color:rgb(3, 45, 67);height:80;padding:10;padding-left:15;">
<font style="font-family:Arial;font-size:300%;font-weight:bold;color:#ffffff;background-color:rgb(3, 45, 67);color:rgb(20, 200, 200);">BI</font>
<font style="font-family:Arial;font-size:300%;font-weight:bold;color:#ffffff;background-color:rgb(3, 45, 67); ">MIR</font><font style="font-family:Arial;">
Condition-specific miRNA target prediction database</font></th>
</tr>
<tr >
<td style="padding:10;padding-left:30;background-color:white;">
<a class="topMenu" href="http://btool.org/bimir_dir/index.html" style="font-size:200%;font-weight:normal;">Home</a> <font style="font-size:200%;font-weight:normal;"> | </font>
<a class="topMenu" href="http://btool.org/bimir_dir/default.php" style="font-size:200%;font-weight:normal;">Search</a> <font style="font-size:200%;font-weight:normal;"> | </font>
<a class="topMenu" href="http://btool.org/bimir_dir/download.html"style="font-size:200%;font-weight:normal;text-decoration:none;">Download</a> <font style="font-size:200%;font-weight:normal;"> | </font>
<a class="topMenu" href="http://btool.org/bimir_dir/help.html"style="font-size:200%;font-weight:normal;">Help</a>
</td>
<td style="background-color:white;" align='right' valign='middle' >
<a href='https://clustrmaps.com/site/1aneh' title='Visit tracker'><img width="140" height="80" src='//clustrmaps.com/map_v2.png?cl=ffffff&w=150&t=tt&d=p7rMVHU-6NMgIb_CzJFxjcboIQd8GHyaJrwr-6mAlLg&co=0049b8&ct=ffffff'/></a>
</td>
</tr>
<tr valign="top" colspan="4" style="background-color:rgb(130, 130, 130);"><td height="3" colspan="4"> </td> </tr>
</table>
</div>
<div>
<ul>
<?php
// $servername = "mysql.hostinger.co.uk";
// $username = "u717682070_admin";
// $password = "xhunter";
// $port = "3306";
// $dbname = "u717682070_mibic";
$servername="117.16.94.203";
$port=3306;
$socket="";
$username="root";
$password="Xhunter@84";
$dbname="bigbicluster";
// Create connection
$conn = new mysqli($servername, $username, $password, $dbname, $port)
or
die("Connection failed: " . $conn->connect_error);
// Retrieve data from Query String
$name = '';
$keyword = '';
$specificgenes = '';
$empty_specgenes = 1;
$specgenelist = '';
$tissue = '';
$disease = '';
$empty_name = 1;
$empty_cond = 1;
$empty_tissue = 1;
$empty_disease = 1;
$query = '';
$qname = '';
$qtissue='';
$qdisease ='';
$qkeyword = '';
$qspecgenes = '';
//var_dump($_POST);
if (isset($_POST['mirna'])){
$name = $_POST['mirna'];
$empty_name = 0;
if ($name == "") {
$name = "ALL";
$qname = "1";
} else {
$qname = "miRNA='".trim($name)."'";
}
}
if (isset($_POST['tissue'])){
$tissue = $_POST['tissue'];
$qtissue = trim($tissue);
if ($qtissue != '')
$empty_tissue = 0;
}
if (isset($_POST['disease'])){
$disease = $_POST['disease']; //echo $disease."<BR><BR>";
$qdisease= trim($disease);
if ($qdisease != '')
$empty_disease = 0;
}
if (isset($_POST['specificgenes'])){
$specificgenes = $_POST['specificgenes']; // remove whitespace trailed\
$qspecgenes = trim($specificgenes); //echo $qspecgenes."<BR><BR>";
if ($qspecgenes != '')
$empty_specgenes = 0;
}
if (isset($_POST['keyword'])){
$keyword = $_POST['keyword']; // remove whitespace trailed\
$qkeyword = trim($keyword); //echo $qkeyword."<BR><BR>";
if ($qkeyword != '')
$empty_cond = 0;
}
$query = "";
if ($empty_tissue && $empty_cond && $empty_disease && $empty_specgenes) {
$query .= "SELECT * FROM bicluster WHERE $qname";
echo "Selected options: <br>miRNA: $name<br><br>";
}
else{
echo "Selected options: <br>* miRNA: $name<br>";
$query .= "SELECT DISTINCT b.* FROM (SELECT * FROM bicluster WHERE $qname ";
if (!$empty_specgenes){
$query .= "AND MATCH (Target) AGAINST ('$qspecgenes' IN BOOLEAN MODE)";
echo "* Specific Genes: $specificgenes<br>";
}
$query .= ") b JOIN (SELECT * FROM totalcondition WHERE 1 ";
$qcond = "";
if (!$empty_tissue){
$qcond .= "AND (conTest LIKE '%$qtissue%' OR conControl LIKE '%$qtissue%' OR conTissue LIKE '%$qtissue%') ";
echo "* Tissue: $tissue<br>";
}
if (!$empty_disease){
$qcond .= "AND (conTest LIKE '%$qdisease%' OR conControl LIKE '%$qdisease%' OR conDisease LIKE '%$qdisease%') ";
echo "* Disease: $disease<br>";
}
if (!$empty_cond){
$qcond .= "AND (MATCH (conTest, conControl) AGAINST ('$qkeyword' IN BOOLEAN MODE)) ";
echo "* Keywords: $keyword<br>";
}
$qcond .= ") t ON FIND_IN_SET (t.conSymbol, b.conSymbol) > 0";
$query .= $qcond;
//echo $query."<BR>";
}
set_time_limit(1000);
ini_set('memory_limit', '256M');
$result = $conn->query($query); // echo "SQL query:<br>$query<br>";
$display_string = '';
if ($result->num_rows <= 0) {
$display_string .= "0 result(s)";
} else {
echo "<br>";
echo "Total ".$result->num_rows." cluster(s) retrieved.<br><br>";
//Build Result String
$display_string .= "<table style='border: 1px solid black;'><tr><th style='border: 1px solid black;'>Name</th><th style='border: 1px solid black;'>miRNA</th><th style='border: 1px solid black;'>Fold</th><th style='border: 1px solid black;'>Size</th>";
$display_string .="<th align='center' style='border: 1px solid black;'> Validated </th>";
if (!$empty_tissue){
$forward_post = "";
if (isset($_POST['mirna'])){
$forward_post .= "<input type='hidden' name='mirna' value='".$_POST['mirna']."'>";
}
if (isset($_POST['tissue'])){
$forward_post .= "<input type='hidden' name='tissue' value='".$_POST['tissue']."'>";
}
if (isset($_POST['disease'])){
$forward_post .= "<input type='hidden' name='disease' value='".$_POST['disease']."'>";
}
if (isset($_POST['specificgenes'])){
$forward_post .= "<input type='hidden' name='specificgenes' value='".$_POST['specificgenes']."'>";
}
if (isset($_POST['keyword'])){
$forward_post .= "<input type='hidden' name='keyword' value='".$_POST['keyword']."'>";
}
$display_string .="<th align='center' style='border: 1px solid black;'>
<form method='post' action='searchp.php' class='inline'>".$forward_post.
"<button type='submit' name='submit_param' value='submit_value' class='link-button' style='text-decoration:none; color:black;font-family:Tahoma;font-size:16;font-weight:bold;'> Proportion </button></form>
</th>";
}elseif (!$empty_disease){
$forward_post = "";
if (isset($_POST['mirna'])){
$forward_post .= "<input type='hidden' name='mirna' value='".$_POST['mirna']."'>";
}
if (isset($_POST['tissue'])){
$forward_post .= "<input type='hidden' name='tissue' value='".$_POST['tissue']."'>";
}
if (isset($_POST['disease'])){
$forward_post .= "<input type='hidden' name='disease' value='".$_POST['disease']."'>";
}
if (isset($_POST['specificgenes'])){
$forward_post .= "<input type='hidden' name='specificgenes' value='".$_POST['specificgenes']."'>";
}
if (isset($_POST['keyword'])){
$forward_post .= "<input type='hidden' name='keyword' value='".$_POST['keyword']."'>";
}
$display_string .="<th align='center' style='border: 1px solid black;'>
<form method='post' action='searchp.php' class='inline'>".$forward_post.
"<button type='submit' name='submit_param' value='submit_value' class='link-button' style='text-decoration:none; color:black;font-family:Tahoma;font-size:16;font-weight:bold;'> Proportion </button></form>
</th>";
}
$display_string .="<th align='center' style='border: 1px solid black;'>Targets</th><th align='left' style='border: 1px solid black;'>Enriched Pathways</th>";
$row2sort = array();
// Insert a new row in the table for each item returned
$odd_line = 1; //
while($row = $result->fetch_assoc()) {
$onerow = "<tr><td valign='top'>" . "<a href='showbc.php?src=j9as1dfhk234cuiihasdfvnkasdh000hkjasdfjkhe89045009345nksaaaajf232hkjasdjfaslkfjalsdf03209234jfllasdfjc09340945&add=".$row["Link"]."&nta=".$row["numTarget"]."&nco=".$row["numCondition"]."&fld=".$row["bimirFold"]."&pas=40zcvzafdaavcljluyinbz19asdfaf81zerqwr413kioiojuooyi41a23sdq54779erq114erqf2354a1239vbcn'>"
. str_replace("_hex_value",'', $row["Name"]). "</a></td><td style='color:red;' valign='top'>"
. str_replace("-", "_", $row["miRNA"]). "</td><td style='color:blue;' align='center' valign='top'>"
. str_replace("_", ".", $row["bimirFold"])
. "</td><td style='color:green;' align='center' valign='top'>".$row["numCondition"]."x".$row["numTarget"]
. "</td><td valign='top' align='center' style='color:magenta;border: 1px solid black;' bgcolor='#FFFFFF'>";
// if ($odd_line%2 == 1){
// $onerow .=
// } elseif ($odd_line%2 == 0) {
// $onerow .= "</td><td valign='top' style='border: 1px solid black;' bgcolor='#DDDDDD'>";
// }
//// evidence
$evidence_rate = 0.0;
$filename = str_replace('-', '.', $row["bimirFold"]).'/'.$row["miRNA"].'/'.str_replace("_hex_value",'', $row["Name"]).'.txt'; //echo $filename;
$evidencePath = str_replace(".txt", "_mtb_evidence.txt", $filename);
$evidenceContent = fopen($evidencePath , 'r' ) or die( "Error in opening file" );
$eviMap = array();
while ($line = fgets($evidenceContent)){
$tmp = preg_split('/\s+/', trim($line));
$eviMap[$tmp[0]] = $tmp[1];
}
fclose( $evidenceContent );
$validatedScore = 0.0;
$curTarget = explode(",", trim($row["Target"]));
foreach ($curTarget as $tg){
if (!strcmp($eviMap[$tg], "S")){
$validatedScore = $validatedScore + 1.0;
}
if (!strcmp($eviMap[$tg], "W")){
$validatedScore = $validatedScore + .6;
}
// if (!strcmp($eviMap[$tg], "-")){
// $validatedScore = $validatedScore + 0;
// }
}
$validatedScore = round($validatedScore / sizeof($curTarget), 4);
$onerow .= $validatedScore."</td>";
if (!$empty_disease || !$empty_tissue){
$onerow .= "<td align='center' valign='top' style='color:orange;border: 1px solid black;'>"; // proportion here
}else
$onerow .= "<td align='left' valign='top' style='color:black;border: 1px solid black;'>"; // no proportion
// proportion here
$rate = 0.0;
if (!$empty_tissue){
$tmp1 = explode(';', trim($row["proportion"]));
foreach($tmp1 as $item){
$term = explode(":", $item); //echo $term[0]."\t".$tissue."<BR>";
if (!strcmp(trim($term[0]), trim($tissue))){
$rate = round((float)$term[1], 4); //echo $rate."<BR>";
break;
}
}
$onerow .= $rate."</td><td valign='top' style='border: 1px solid black;'>"; // proportion here
} elseif (!$empty_disease){
$tmp1 = explode(';', trim($row["disease"]));
if ($disease === "Alzheimer") $disease = "Alzheimer's disease";
foreach($tmp1 as $item){
$term = explode(":", $item); //echo $term[0]."\t".$tissue."<BR>";var_dump($term);
if ($term[0] !== '') { //var_dump($disease);
if (!strcmp(trim($term[0]), trim($disease))){
$rate = round((float)$term[1], 4); //echo $rate."<BR>";
break;
}
}
}
$onerow .= $rate."</td><td valign='top' style='border: 1px solid black;'>"; // proportion here
}
// highlight $qspecgenes
$curTarget = explode(",", trim($row["Target"]));
$globalSpecGenes = explode(" ", str_replace(array('+', '-'),'',trim($qspecgenes)));
$resTarget = "";
foreach ($curTarget as $tg){
$matchhere = 0;
foreach ($globalSpecGenes as $sg){
if (!strcmp(trim($tg), trim($sg))){
$resTarget .= "<mark><b>".$tg."</b></mark>, ";
$matchhere = 1;
break;
}
}
if (!$matchhere){
$resTarget .= $tg.", ";
}
}
$onerow .= $resTarget. "</td><td valign='top' style='border: 1px solid black;' bgcolor='#FFFFFF'>";
// if ($odd_line%2 == 1){
// } elseif ($odd_line%2 == 0) {
// $onerow .= $resTarget. "</td><td valign='top' style='border: 1px solid black;' bgcolor='#DDDDDD'>";
// }
// $odd_line ++;
// enriched pathways
$onerow .= "<div class='comment more'>";
$filename = $row["Link"];
$enriched_c2 = str_replace(".txt", "_c2_enriched.txt", $filename);
$enriched_c5 = str_replace(".txt", "_c5_enriched.txt", $filename);
$long_or_not = 0; /// 1 is long
if (file_exists($enriched_c2)){
$enrichedContent = fopen($enriched_c2 , 'r' ) or die( "Error in opening file" );
$tmp = fgets($enrichedContent); // remove header line
$count_to_N = 0; // N = 3
while ($line = fgets($enrichedContent)){
$tmp = preg_split('/\s+/', trim($line));
$onerow .= $tmp[0]." (C2)<br>";//"<a href='http://software.broadinstitute.org/gsea/msigdb/cards/".$tmp[0].".html'>".$tmp[0]." (C2)</a> <br>";
if (++$count_to_N == 3){
$onerow .= "<span class='morecontent'><span>";
}
}
if ($count_to_N > 3){
$onerow .= "</span><div class='text-center margin_top_10'><a href='' class='morelink'>More (+)</a></div></span></div>";
}
fclose( $enrichedContent );
}
if (file_exists($enriched_c5)){
$enrichedContent = fopen($enriched_c5 , 'r' ) or die( "Error in opening file" );
$tmp = fgets($enrichedContent); // remove header line
$count_to_N = 0; // N = 3
while ($line = fgets($enrichedContent)){
$tmp = preg_split('/\s+/', trim($line));
$onerow .= $tmp[0]." (C5)<br>";//"<a href='http://software.broadinstitute.org/gsea/msigdb/cards/".$tmp[0].".html'>".$tmp[0]." (C5)</a> <br>";
if (++$count_to_N == 3){
$onerow .= "<span class='morecontent'><span>";
}
}
if ($count_to_N > 3) {
$onerow .= "</span><div class='text-center margin_top_10'><a href='' class='morelink'>More (+)</a></div></span></div>";
}
fclose( $enrichedContent );
}
// finish a row
$onerow .="</td><td valign='top'></td></tr>";
////////////////////////////////////////////////////////
// selection
$row2sort["$onerow"] = $validatedScore;//$rate;
}
// Sorting based on proportion high to low
arsort($row2sort);
foreach($row2sort as $key => $val){
$display_string .= $key;
}
$display_string .= "</table>";
}
$conn->close();
echo $display_string;
?>
<br><br>
<button onclick="goBack()">Go Back</button><br><br>
<a href="mailto:[email protected]" target="_blank"><img src="./index_files/mail.png" align="middle" border="0" ></a>
</ul>
<br>
<br>
<br>
</div>
<div class="footer">
<table border="0" width="100%" colspan="100%" style="border-spacing:0;" >
<tr valign="top" style="background-color:rgb(20, 120, 120);">
<td height="15"> </td>
</tr>
<tr valign="top" colspan="2" style="background-color:rgb(3, 45, 67);">
<td height="30"> </td>
</tr>
</table>
</div>
</body></html>