BioPHP: PHP for Biocomputing

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Source Code Listing for restcut_par.php

Note: This uses unreleased BioPHP 1.1 code. Attempting to run this with 1.0 may result in some unexplained or unpredictable behavior. Also, what you'll see here is simply the PHP script inside restcut_par.php, and not the entire file. The rest of the file is in plain HTML.

// This code was written by Serge Gregorio, Jr. (serge525@hotmail.com) 
// and is under the General Public License (GPL) 2.0 license.

// This "populates" the listbox with names and recognition patterns of restriction enzymes.
<select name="re">
   <option></option>
   <?php
      require_once("resten.inc");
			
      $re_list = array_keys($RestEn_DB);			
      foreach($re_list as $re)
         {
         $re_info = $RestEn_DB[$re];
         $pat = $re_info[0];
         print "<option value=$re>$re --- $pat</font></option>"; 
         }
   ?>
</select>

Source Code Listing for restcut_res.php

Note: This uses unreleased BioPHP 1.1 code. Attempting to run this with 1.0 may result in some unexplained or unpredictable behavior.

// This code was written by Serge Gregorio, Jr. (serge525@hotmail.com) 
// and is under the General Public License (GPL) 2.0 license.

<html>
<head><title>Find Fragments from Restriction Enzyme Digest - Results Page</title></head>
<body bgcolor=#FFFFCC>
   <h1>Find Fragments from Restriction Enzyme Digest</h1>
   <h1>Results Page</h1>
   <?php
      // tools.inc is part of GenePHP 1.1.
      require_once("tools.inc");

      $seqo = new Seq();
      $seqo->sequence = strtoupper($nucseq);

      $reo = new RestEn("'name'=>'" . $re . "'");

      // CutSeq() method of RestEn class in GenePHP 1.0 has been renamed to cut() in GenePHP 1.1.
      $frags = $reo->cut($seqo);
      print "<center>";

      // cut_tab() outputs the result of the cut() method to a pre-designed HTML table.  It is part of tools.inc and GenePHP 1.1.
      cut_tab($frags, $re);
      print "</center>";
   ?>
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</body>
</html>

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