Return
$end)
{die("chromosome start position is greater than end position!");}
$con = mysql_connect("localhost","root2","SMUCKrasp23");
if (!$con)
{
die('Could not connect: ' . mysql_error());
}
mysql_select_db("dasr", $con)
or die ("could not select database!");
if ($chr=="All chromosomes" and !$start and !$end)
$query = "";
if (!$start and !$end and $chr != "All chromosomes")
$query = "WHERE chrom = '$chr'";
if ($start or $end)
$query= "WHERE chrom = '$chr' AND chromstart> $start AND chromend< $end;";
if ($bedfile_id)
$query = "WHERE bedfile_id=$bedfile_id and chrom = '$chr';";
if ($bedfile_id and $chr == "All chromosomes" )
$query = "WHERE bedfile_id=$bedfile_id;";
if ($action=="Count Reads"){
$result = mysql_query("Select count(*) from summarybed $query;");
$row = mysql_fetch_row($result);
$table1 = $row[0];
print "The file you have chosen is: $bedfile_id
";
print "Chromosome: $chr
";
print "Position $start to $end
";
print "Query result: $table1
";
#print "End of the if statement for Count Reads";
}
if ($action=="View Reads across all chromosomes"){
$result = mysql_query("select chrom, count(*) From summarybed where bedfile_id = $bedfile_id Group by chrom order by chrom;");
//printing the table
echo "";
echo "
| chrom |
count(*) |
";
$count = array();
$chr = array();
while($row = mysql_fetch_array($result)){
echo "";
echo "| " . $row['chrom'] . " | ";
echo "" . $row['count(*)'] . " | ";
array_push($count,$row['count(*)']);
array_push($chr,$row['chrom']);
echo "
";
}
echo "
";
//After printing the table, want to give the total number of reads
//Want to return the total count for the file (same as above)
$total_read = mysql_query("Select count(*) from summarybed WHERE bedfile_id=$bedfile_id;");
//Need to get the number from the resulting query
$row_total_read = mysql_fetch_row($total_read);
$total_read_number = $row_total_read[0];
print "Total number of reads for this BED file is: $total_read_number
";
//Creating the pie chart
$count_str = join(",",array_values($count));
$chr_str = join("|",array_values($chr));
$color_inx1 = rand(0,2);
$color_inx2 = $color_inx1 +1;
$color_array = array("FF0000","0000FF","00FF00","BB0000");
//print (gettype($count_str));
$chart1 = "
";
print $chart1;
}//end of the if statement
mysql_close($con);
exit;
?>