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gene_locus_search.php
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gene_locus_search.php
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Gene view</title>
<link rel="stylesheet" type="text/css" href="./css/header.css">
<link rel="stylesheet" type="text/css" href="./css/content.css">
<link rel="stylesheet" type="text/css" href="./css/footer.css">
<link rel="stylesheet" type="text/css" href="./DataTables/DataTables-1.10.18/css/jquery.dataTables.min.css">
<link rel="stylesheet" type="text/css" href="./DataTables/Buttons-1.5.4/css/buttons.dataTables.min.css">
<script type="text/javascript" src="DataTables/jQuery-3.3.1/jquery-3.3.1.min.js"></script>
<script type="text/javascript" src="./DataTables/DataTables-1.10.18/js/jquery.dataTables.min.js"></script>
<script type="text/javascript" src="./DataTables/Buttons-1.5.4/js/dataTables.buttons.min.js"></script>
<script type="text/javascript" src="./DataTables/pdfmake-0.1.36/pdfmake.min.js"></script>
<script type="text/javascript" src="./DataTables/JSZip-2.5.0/jszip.min.js"></script>
<script type="text/javascript" src="./DataTables/Buttons-1.5.4/js/buttons.flash.min.js"></script>
<script type="text/javascript" src="./DataTables/pdfmake-0.1.36/vfs_fonts.js"></script>
<script type="text/javascript" src="./DataTables/Buttons-1.5.4/js/buttons.html5.min.js"></script>
</head>
<body>
<div class="heading">
Botrytis Cynerea Database
</div>
<div class="main">
<div class="content" id="gene_search">
<?php
if (preg_match("/BC1G_/", $_POST['gene_number'])) {
$gene_locus = "$_POST[gene_number]";
} else {
$gene_locus = "BC1G_$_POST[gene_number]";
}
// echo "$gene_locus</br>"; // TEST
// Query
try {
$dbh = new PDO('mysql:host=localhost;dbname=botrytis', 'lespinet', '');
$query_gene = $dbh->query('SELECT gene_locus, gene_seq, gene_start, gene_stop, gene_length, gene_strand, gene_supercontig, gene_operon, trans_id FROM gene WHERE gene_locus = "'.$gene_locus.'";');
while ($row = $query_gene->fetch(PDO::FETCH_ASSOC)) {
// print_r($row); // TEST
$locus = $row['gene_locus'];
$seq = $row['gene_seq'];
$start = $row['gene_start'];
$stop = $row['gene_stop'];
$length = $row['gene_length'];
$strand = $row['gene_strand'];
$supercontig = $row['gene_supercontig'];
$operon = $row['gene_operon'];
$trans = $row['trans_id'];
}
$query_prot = $dbh->query('SELECT prot_name,prot_seq, prot_length FROM protein WHERE gene_locus = "'.$locus.'" AND trans_id = "'.$trans.'";');
while ($line = $query_prot->fetch(PDO::FETCH_ASSOC)) {
// print_r($row);
$prot_name = $line['prot_name'];
$prot_seq = $line['prot_seq'];
$prot_length = $line['prot_length'];
}
} catch (PDOException $e) {
echo "Erreur ! " . $e->getMessage() . "<br/>";
die();
} catch (Exception $ee) {
echo "Erreur ! " . $ee->getMessage() . "<br/>";
die();
}
// $columns = array($locus, $seq, $start, $stop, $length, $strand, $supercontig, $operon, $trans);
// foreach ($columns as $key => $value) {
// echo $key . " : " . $value . "</br>";
// }
?>
<script>
$(document).ready(function() {
$('#table_gene').DataTable( {
dom: 'Bfrtip',
buttons: [
'copy', 'csv', 'pdf'
]
} );
} );
</script>
<table id="table_gene" class="display" style="align:center">
<tbody>
<tr>
<td><b>Gene Locus</b></td>
<td colspan="2"><?php echo $locus ?></td>
</tr>
<tr>
<td><b>Sequence</b></td>
<td colspan="2" style="word-break: break-all">
<?php echo $seq ?></br>
</td>
</tr>
<tr>
<td><b>Start</b></td>
<td colspan="2"><?php echo $start ?></td>
</tr>
<tr>
<td><b>Stop</b></td>
<td colspan="2"><?php echo $stop ?></td>
</tr>
<tr>
<td><b>Length</b></td>
<td colspan="2"><?php echo $length ?></td>
</tr>
<tr>
<td><b>Strand</b></td>
<td colspan="2"><?php echo $strand ?></td>
</tr>
<tr>
<td><b>Supercontig</b></td>
<td colspan="2"><?php echo $supercontig ?></td>
</tr>
<tr>
<td><b>Transcript ID</b></td>
<td colspan="2"><?php echo $trans ?></td>
</tr>
<!-- Display Protein informations -->
<tr>
<td><b>Protein name</b></td>
<td colspan="2"><?php echo $prot_name ?></td>
</tr>
<tr>
<td><b>Protein Sequence</b></td>
<td colspan="2" style="word-break: break-all">
<?php echo $prot_seq ?>
</td>
</tr>
<tr>
<td><b>Protein Length</b></td>
<td colspan="2"><?php echo $prot_length ?></td>
</tr>
<?php
if ($operon != "") {
$pfam = preg_split("/;/", $operon);
echo
'<th scope="rowgroup" rowspan="'.(count($pfam)*8+1).'">
<b>Pfam</b>
</th>';
foreach ($pfam as $key => $value) {
// Link to Pfam website
echo '
<tr>
<th scope="colgroup" colspan="2">
<a href="https://pfam.xfam.org/family/'.$value.'" target="_blank" title="Pfam webpage of '.$value.'">'.$value.'</a>
</th>';
try {
$query_pfam = $dbh->query('SELECT MIN(id), pfam_name, pfam_description, pfam_start, pfam_stop, pfam_length, pfam_score, pfam_expected FROM pfam WHERE pfam_locus = "'.$locus.'" AND prot_name = "'.$prot_name.'" AND pfam_acc = "'.$value.'";');
while ($l = $query_pfam->fetch(PDO::FETCH_ASSOC)) {
// print_r($row); // TEST
$pfam_name = $l['pfam_name'];
$pfam_desc = $l['pfam_description'];
$pfam_start = $l['pfam_start'];
$pfam_stop = $l['pfam_stop'];
$pfam_length = $l['pfam_length'];
$pfam_score = $l['pfam_score'];
$pfam_eval = $l['pfam_expected'];
}
} catch (PDOException $e) {
echo "Erreur ! " . $e->getMessage() . "<br/>";
die();
} catch (Exception $ee) {
echo "Erreur ! " . $ee->getMessage() . "<br/>";
die();
}
// Display the Pfam results foreach Pfam accession id
echo '
<tr>
<td><b>
Name
</b></td>
<td>
'.$pfam_name.'
</td>
</tr>
<tr>
<td><b>
Description
</b></td>
<td>
'.$pfam_desc.'
</td>
</tr>
<tr>
<td><b>
Start
</b></td>
<td>
'.$pfam_start.'
</td>
</tr>
<tr>
<td><b>
Stop
</b></td>
<td>
'.$pfam_stop.'
</td>
</tr>
<tr>
<td><b>
Length
</b></td>
<td>
'.$pfam_length.'
</td>
</tr>
<tr>
<td><b>
Score
</b></td>
<td>
'.$pfam_score.'
</td>
</tr>
<tr>
<td><b>
E-value
</b></td>
<td>
'.$pfam_eval.'
</td>
</tr>
</tr>';
}
}
?>
</tbody>
</table>
<!-- <?php
// exec('"C:/Program Files/R/R-3.5.2/bin/Rscript.exe" "C:/wamp64/www/botrytis/data/hydro.r" "'.$prot_seq.'" 21', $result);
?>
<img src="data/hydro.jpg"> -->
</div>
</div>
<div class="footer">
<p>Botrytis cinerea Database 2019</p>
</div>
</body>
</html>