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lsatPrimerSearch.php
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lsatPrimerSearch.php
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html dir="ltr" xmlns="http://www.w3.org/1999/xhtml">
<head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Lsat | SSR Primer</title>
<link rel="shortcut icon" href="icon1.png">
<link href="Lsatv1.css" rel="stylesheet" type="text/css">
<style>
.csvtab{
table-layout: fixed;
width:100%;
border-collapse: collapse;
border: 2px blue solid;
font: 12px sans-serif;
}
.csvtr{
background: #ee9;
color:black;
font: 15px sans-serif;
}
table.display th{ background: #D5E0CC; }
table.display td{ background: #fff;
border: 1px green solid;
padding: 5px;
word-wrap: break-word;
}
table.responsive-table{
box-shadow: 0 10px 20px rgba(0, 0, 0, 0.3);
}
</style>
<style type="text/css">
a:link {color:#BCC0BB; background-color:transparent; text-decoration:none}
a:visited {color:pink; background-color:transparent; text-decoration:none}
a:hover {color:blue; background-color:transparent; text-decoration:underline}
a:active {color:yellow; background-color:transparent; text-decoration:underline}
</style>
</head>
<body>
<div id="wrapper">
<header>
<table>
<td>
<img alt="LsatLogo" height="120" src="lsatlogo.png" width="121" />
</td>
<td>
Lsat: web-based micro-satellite analysis tool for family Liliaceae
</td>
</table>
</header>
<div style="padding-top:2px">
<table style="width:100%">
<tr>
<td id="left" style="width:30%;">
<h2> SSR Primer Design Summary</h2>
<?php
// get SSR search parameter and data file name
$fname = $_GET['datafilename'];
// echo $fname; echo '<br>';
// this block is ok -------------->
// system("perl /opt/lampp/htdocs/Lsat/LsatMISA.pl /opt/lampp/htdocs/Lsat/SSROutPut/$db_file"); // SSR search perl script call
// Primer3 input data file generate
// P3 input file name
$piname="$fname".".SSR"; //echo $piname; echo '<br>';
// P3in perl Running -------->
system ("perl /opt/lampp/htdocs/Lsat/lsatp3in.pl /opt/lampp/htdocs/Lsat/SSROutPut/$piname");
// primer3 exe input file name creates
//echo '<br>';
$pexeinfn="$piname".".p3in";
$hrik="/opt/lampp/htdocs/Lsat/SSROutPut/$pexeinfn";
$x="$piname".".p3out";
$primercoreoutfn="/opt/lampp/htdocs/Lsat/SSROutPut/$x";
system ("primer3_core < $hrik> $primercoreoutfn ");
// echo "RUN p3out "; echo '<br>';
//--------------------------------->
//Primer3 output generating
system ("perl /opt/lampp/htdocs/Lsat/lsatp3out.pl /opt/lampp/htdocs/Lsat/SSROutPut/$x /opt/lampp/htdocs/Lsat/SSROutPut/$piname");
$linkprimer ="$piname".".CSV";
$ssrmarker="$piname".".results";
?>
<br><br>
<h3> SSR Primer download</h3>
<a href="/Lsat/SSROutPut/<?php echo "$linkprimer"?>" download> Download SSR Primer [sequences]</a>
<br>
<!-- <a href="/Lsat/SSROutPut/<?php echo "$ssrmarker"?>" download> Download SSR Primer database [detail]</a> --->
</td>
<td id="right" style="width:30%; float:left">
<h2> SSR Primer Display </h2>
<div style="width: 850px; height: 450px; overflow: scroll">
<?php
echo "<table class='csvtab display responsive-table'>\n\n";
$flnp ="$piname".".CSV";
//echo $flnp;
$flnpx="./SSROutPut/$flnp";
$f = fopen($flnpx, "r") or die("Unable to open csv file!");
echo "<thead >";
echo "<tr class='csvtr' >";
echo "<td style='background: #ee9; width: 180px; height: 20px;'>Seq ID</td>";
echo "<td style='background: #ee9; width: 100px;'>SSR ID</td>";
echo "<td style='background: #ee9; width: 200px;'>F Primer</td>";
echo "<td style='background: #ee9; width: 200px;'>R Primer</td>";
echo "<td style='background: #ee9;'>PCR Product</td>";
/*echo "<td style='background: #ee9;'>SSR Class</td>";
echo "<td style='background: #ee9;'> motif Rich in</td>";
echo "<td style='background: #ee9; width: 400px; height: 20px;'>Flanking Seq</td>";*/
echo "</tr >";
echo "</thead>";
echo "<tbody>";
while (($line = fgetcsv($f, 0, "\t")) !== false) {
echo "<tr >";
foreach ($line as $cell) {
echo "<td class='csvtd'>" . htmlspecialchars($cell) . "</td>";
}
echo "</tr>\n";
}
fclose($f);
echo "</tbody>";
echo "\n</table>";
?>
</div>
</td>
</tr>
<tr><td collspan="2" id="bottom">
<table>
<tr>
<td style="width:70%; padding-left:120px;">
<span style="color:yellow">Cite US: </span> Biswas et al (2018) Lsat: web-based micro-satellite analysis tool for family Liliaceae.
http://210.110.86.160/Lsat/Lsat.html <br>
<span style="color:yellow">Contuct US: </span> [email protected] <br>
</td>
<td style="width: 40%">
<span style="color:yellow">Useful Link </span><br> <a href="http://210.110.86.160/Lidb/Lilidb_Home.html"> Lili-db </a><br>
</td>
<td style="width: 10%">
</td>
</tr>
</table>
</td></tr>
</table>
</div>
</div>
</body>
</html>