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gene_search.php
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="">
<meta name="author" content="">
<title>Group A Steered Research Project</title>
<!-- Bootstrap Core CSS -->
<link href="CSS/bootstrap.min.css" rel="stylesheet">
<!-- Custom CSS -->
<link href="CSS/4-col-portfolio.css" rel="stylesheet">
<!-- Bootstrap JS -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
<!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
<script src="https://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<body background="Images/geometry.png">
<!-- Navigation -->
<nav class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Project Webserver</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav">
<li>
<a href="background.html">Analysis Summary</a>
</li>
<li class="dropdown"><a class="dropdown-toggle" data-toggle="dropdown" href="#">Data<span class="caret"></span></a>
<ul class="dropdown-menu">
<li><a href="gene_search.php">Expression Levels</a></li>
<li><a href="diff_exp.php">Differential Expression</a></li>
<li><a href="graph_data.html">Volcano Plot with R Shiny</a></li>
<li><a href="search_ucsc.php">Visualise Mapped Data</a></li>
<li><a href="fastqc.html">View FastQC Files</a></li>
</ul>
</li>
<li>
<a href="team.html">Team</a>
</li>
</ul>
</div>
<!-- /.navbar-collapse -->
</div>
<!-- /.container -->
</nav>
<!-- Page Content -->
<div class="container">
<!-- Page Heading -->
<div class="row">
<div class="col-lg-12">
<h1 class="page-header">Search Gene Expression Level Data
</h1>
<?php
// Insert connection details from config-file.ini
$db = parse_ini_file("../config-file.ini");
$host = $db['host'];
$user = $db['user'];
$pass = $db['pass'];
$name = $db['name'];
// Create connection
$conn = new mysqli($host, $user, $pass, $name);
// Check connection
if ($conn -> connect_error) {
$message = $conn -> connect_error;
}
else {
$message = "Connection successful";
}
?>
<?php
$find_genome_ids = 'SELECT DISTINCT(genome) FROM FPKM_and_counts;';
$result = $conn->query($find_genome_ids);
?>
<?php
$find_trim_status = 'SELECT DISTINCT(trim_status) FROM FPKM_and_counts;';
$result_trim = $conn->query($find_trim_status);
?>
<?php
$find_pipeline_id = 'SELECT DISTINCT(pipeline) FROM FPKM_and_counts;';
$result_pipeline = $conn->query($find_pipeline_id);
?>
<!-- HTML form created using variable data from MySQL table -->
<form action="<?php echo htmlspecialchars("gene_search.php")?>" method="post">
<div class="input-group" style="width: 40%; float: left">
<input type=text name="search" placeholder="Enter gene name to search" class="form-control">
<div class="input-group-btn">
</div>
</div>
<select style="height: 2.4em; width: 10em;" name="genome_id">
<option value='All'>All Genomes</option>
<?php while ($row = $result -> fetch_object()): ?>
<option value='<?php echo $row->genome; ?>'><?php echo $row->genome; ?></option>
<?php endwhile; ?>
</select>
<select style="height: 2.4em; width: 15em;" name="trim_status_id">
<option value='All'>Trimmed And Untrimmed</option>
<?php while ($row = $result_trim -> fetch_object()): ?>
<option value='<?php echo $row->trim_status; ?>'><?php echo $row->trim_status; ?></option>
<?php endwhile; ?>
</select>
<select style="height: 2.4em; width: 10em;" name="pipeline_id">
<option value='All'>All Pipelines</option>
<?php while ($row = $result_pipeline -> fetch_object()): ?>
<option value='<?php echo $row->pipeline; ?>'><?php echo $row->pipeline; ?></option>
<?php endwhile; ?>
</select>
<button type="submit" class="btn btn-default">Submit</button>
</form>
<?php
$input = "";
$len = "";
$result = "";
$table = "";
if ($_SERVER["REQUEST_METHOD"] == "POST") {
$input = htmlspecialchars($_POST["search"]);
$genome_input = htmlspecialchars($_POST["genome_id"]);
$trim_input = htmlspecialchars($_POST["trim_status_id"]);
$pipeline_input = htmlspecialchars($_POST["pipeline_id"]);
}
$len = strlen($input);
if ($len >= 3) {
// When user types in a query and selects dropdown options, data from the MySQL table populates a PHP generated table
$sql = "SELECT * FROM FPKM_and_counts WHERE gene_short_name LIKE \"%$input%\"";
if ($genome_input != 'All') {
$sql = $sql . " AND genome='$genome_input'";
}
if ($trim_input != 'All') {
$sql = $sql . " AND trim_status='$trim_input'";
}
if ($pipeline_input != 'All') {
$sql = $sql . " AND pipeline='$pipeline_input'";
}
$result = $conn->query($sql);
if (!$result) {
printf("Error: %s\n", $conn->error);
$table = "<strong>No results</strong>";
}
else {
$table = "";
if ($input) {
if ($result->num_rows > 0) {
// PHP generated table to hold MySQL data
$table = "<thead><tr> <th>Select</th> <th>Gene Name</th> <th>Genome</th> <th>Trim Status</th> <th>Pipeline</th> <th>Rat 7973 FPKM/Counts</th><th>Rat 8050 FPKM/Counts</th><th>Rat 8043 FPKM/Counts</th><th>Rat 8033 FPKM/Counts</th><th>Rat 8059 FPKM/Counts</th> </tr></thead>";
while ($row = $result -> fetch_assoc()) {
$table .= "<tbody><tr><td>".$row["click"]."<a target='_blank' href='http://www.sigmaaldrich.com/catalog/genes/".$row["gene_short_name"]."?lang=en®ion=GB'><button type='button' class='btn btn-default btn-xs'>Gene Information</button></a><br><a target='_blank' href='gene_view.php?gene=".$row["gene_short_name"]."&genome=".$row["genome"]."&trim_status=".$row["trim_status"]."&pipeline=".$row["pipeline"]."'><button type='button' class='btn btn-default btn-xs'>Plotly Bar Chart</button></a></td><td>".$row["gene_short_name"]."</a></td><td>".$row["genome"]."</td><td>".$row["trim_status"]."</td><td>".$row["pipeline"]."</td><td>".$row["rat_7973"]."</td><td>".$row["rat_8050"]."</td><td>".$row["rat_8043"]."</td><td>".$row["rat_8033"]."</td><td>".$row["rat_8059"]."</td></tr>";
}
$table .= "</tbody>";
}
else {
$table = "<strong>No results</strong>";
}
}
}
}
else {
print "<p style='clear: both;'>Please enter at least 3 characters.</p>";
}
?>
<?php $conn->close();?>
<div class="table-responsive">
<table class="table"><?php echo $table;?></table>
</div>
<span class="col-sm-2"></span>
</div>
</div>
<!-- /.row -->
<br><br><br><br><br><br><br><br><br><br><br><br>
<hr>
<!-- Footer -->
<footer>
<div class="row">
<div class="col-lg-12">
<p>Group A Steered Research Project - MSc Bioinformatics @ University of Leicester - 2017</p>
</div>
</div>
<!-- /.row -->
</footer>
</div>
<!-- /.container -->
<!-- jQuery -->
<script src="js/jquery.js"></script>
<!-- Bootstrap Core JavaScript -->
<script src="js/bootstrap.min.js"></script>
</body>
</html>