$end) {die("chromosome start position is greater than end position!");} $header = "track name = $track description = '$description' itemRgb='$color'\n"; //print "The file you have chosen is: $file1
"; //print "Chromosome: $chr
"; //print "Position $start to $end
"; $order=""; $con = mysql_connect("localhost","root2","SMUCKrasp23"); if (!$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< $end;"; if ($chr and $start and $end and $rgb1 and $rgb2 and $rgb3) $query= "WHERE chrom = '$chr' AND chromstart> $start AND chromend< $end and itemrgb='$rgbquery'"; if (!$chr and !$start and !$end and $rgb1 and $rgb2 and $rgb3) $query= "WHERE itemrgb='$rgbquery'"; if ($chr and !$start and !$end and $rgb1 and $rgb2 and $rgb3) $query= "WHERE chrom = '$chr' AND itemrgb='$rgbquery'"; if ($sort=="Position") $order="ORDER BY chrom $sortmethod,chromstart $sortmethod"; if ($sort=="RGB") $order="ORDER BY itemrgb $sortmethod"; if (!$sort) $order=""; $result = mysql_query("SELECT * FROM $file1 $query $order ;"); if ($action=="Download bed file"){ $new_extract = "temp/$id"."$extension"; system("chmod a+x 777 $new_extract"); $fh=fopen($new_extract,"w") or die ("cannot open file"); fwrite($fh, "$header"); while($row = mysql_fetch_array($result)) { fwrite($fh,"$row[chrom]\t$row[chromstart]\t$row[chromend]\t$row[name]\t$row[score]\t$row[strand]\t$row[thickstart]\t$row[thickend]\t$row[itemrgb]\t$row[blockcount]\t$row[blocksizes]\t$row[blockstarts]\n"); } fclose($fh); echo "DASR_extract/"."$new_extract"; } if ($action=="View bed file"){ echo "$header"; echo ""; echo ""; while($row = mysql_fetch_array($result)){ echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; echo ""; } echo "

summarybed_id	bedfile_id	chrom	chromstart	name	score	strand	thickstart	thickend	itemrgb	blockcount	blocksizes	blockstarts
" . $row['summarybed_id'] . "	" . $row['bedfile_id'] . "	" . $row['chrom'] . "	" . $row['chromstart'] . "	" . $row['chromend'] . "	" . $row['name'] . "	" . $row['score'] . "	" . $row['strand'] . "	" . $row['thickstart'] . "	" . $row['thickend'] . "	" . $row['itemrgb'] . "	" . $row['blockcount'] . "	" . $row['blocksizes'] . "	" . $row['blockstarts'] . "

"; } //$csv_output = "column 1,column2"; //$csv_output .= "\n"; //$output=""; //while($row = mysql_fetch_array($result)) { //$output .= "$row[summarybed_id]\t$row[bedfile_id]\t$row[chrom]\t$row[chromstart]\t$row[chromend]\t$row[name]\t$row[score]\t$row[strand]\t$row[thickstart]\t$row[thickend]\t$row[itemrgb]\t$row[blockcount]\t$row[blocksizes]\t$row[blockstarts]\n"; // } //header("Content-type: application/BED"); //header("Content-disposition: BED" . ".BED"); //print $output; mysql_close($con); exit; ?>