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BioPHP - GC Contenf Finder

Original code submitted by renji143
Code bellow is covered by GNU GPL v2 license.

Description

Last change: 2011/04/27 11:01 | Recent Changes | Original description

The Percentage of Guanine-Cytosine in a Nucleotide sequence determines the
stability of the sequence

Code

Last change: 2011/04/27 11:01 | Recent Changes | Download | Original code

# ========================================================
#
# Author : Renjith.R, Kerala
# license   GNU GPL v2
# Please Make a folder uploads in root
# This work is Done by Renjith.R, Research Officer, bioWORLD
# 
#
# ========================================================
<form enctype="multipart/form-data" action="<?php echo $_SERVER['PHP_SELF'];?>" method="POST">
  <p><strong>Upload Nucleotide Sequence in Fasta format to upload </strong></p>
  <p>Important: Please use only txt files The file should contain only Letters </p>
  <table> 
    <tr>
      <td colspan="2"><input name="uploadedfile" type="file" /></td>
    <tr>
    <td width="137"><input type="hidden" name="MAX_FILE_SIZE" value="100000" />
    : 
    
    <br /></td>
    <td width="79"><input name="submit" type="submit" value="Upload File" /></td>
    </table> 
</form>
Source code is available at<a href=http://www.biophp.org/minitools/minitool_name>BioPHP.org</a>
<?php

echo "<br>";
function IsValidSequence($sequence)
{
	$length = strlen($sequence);
	for ($i=0;$i<$length;++$i)
	{
		if(	!($sequence[$i]=='a' || $sequence[$i]=='A'|| 
			$sequence[$i]=='t'|| $sequence[$i]=='T' || 
			$sequence[$i]=='g'|| $sequence[$i]=='G'|| 
			$sequence[$i]=='c'|| $sequence[$i]=='c'))
			{
				return false;
			}
			else return true;
	}
	
}
echo $_POST['uploadedfile'];
$target_path = "uploads/";

$target_path = $target_path . basename( $_FILES['uploadedfile']['name']); 

if(move_uploaded_file($_FILES['uploadedfile']['tmp_name'], $target_path)) {
    echo "The file ".  basename( $_FILES['uploadedfile']['name']). 
    " has been uploaded";
} else{
    echo " Please Upload the file";
}


$target_path = "uploads/";

$target_path = $target_path . basename( $_FILES['uploadedfile']['name']); 

if(move_uploaded_file($_FILES['uploadedfile']['tmp_name'], $target_path)) {
    echo "The file ".  basename( $_FILES['uploadedfile']['name']). 
    " has been uploaded"; 
} 
echo "<br>";

mysql_connect('localhost','root','');
$myFile = "uploads/" . basename( $_FILES['uploadedfile']['name']) ;
$fh = fopen($myFile, 'r');
$var = fread($fh, 1000000);
//echo $var;
fclose($fh);


$length = strlen($var);
//echo $var[0];
//echo $var[0];
//echo "<br>";
if($length!='')
{

if(IsValidSequence($var))
		{
		
//$a=0;$g=0;$t=0;$c=0;
for ($i=0;$i<$length;++$i)
{
	
			switch($var[$i])
		{
			case 'a':
			case 'A':
				$a++;
				break;
			case 't':
			case 'T':
				$t++;
				break;
		
			case 'c':
			case 'C':
				$c++;
				break;
			
			case 'g':
			case 'G':
				$g++;
				 
		}
		}
echo "<br>";
echo "Total Length of Sequence is $length";
echo "<br>";
echo "Number of A = $a";
echo "<br>";
echo "Number of  T= $t";
echo "<br>";
echo "Number of G = $g";
echo "<br>";
echo "Number of C= $c";
echo"<br>";
$at= (($a+$t)/$length)*100;
echo "% of at =$at";
echo"<br>";
$gc= (($g+$c)/$length)*100;
echo "% of gc =$gc";
}
else
echo "Please check....This is not a Nucleotide sequense";
}
?>