"; print "Tables;$table1 $table2
"; $table1 = $table1."_real"; $q3 = "select chrom,chromstart,chromend,name,score,strand from $table1 where bedfile_id = $bedfile_id1 order by chrom,chromstart into outfile \"/var/www/DASR_2011/DASR_compare/temp/1_$filename1\""; $table2 = $table2."_real"; $q4 = "select chrom,chromstart,chromend,name,score,strand from $table2 where bedfile_id = $bedfile_id2 order by chrom,chromstart into outfile \"/var/www/DASR_2011/DASR_compare/temp/2_$filename2\""; mysql_query($q3) or die ("Error q3!"); mysql_query($q4) or die ("Error q4!"); #################### Run bedtool ######################### $temp = "temp/result.bed"; $action = "/var/www/DASR_2011/BEDTools-Version-2.11.2/bin/intersectBed -wao -a temp/1_$filename1 -b temp/2_$filename2 > $temp"; // original overlapped file system($action); // call BEDTools ############### Get cutoff processed file(combined columns)################ $random_number = genRandomString(); print "
Please Keep Your Retrieval ID: $random_number
"; $new_file = "temp/$random_number"."_combinedcolumns".".txt"; //combined columns overlaps_cut($new_file,$temp,$overlaps); function overlaps_cut($new_file,$temp,$overlaps) { $fh =fopen($temp,"r") or exit("Unable to open $temp!"); // read from an original overlapped file, $temp $fh1=fopen($new_file,"w") or exit("Unable to write $new_file!"); // write into a new overlapped file while(!feof($fh)) { $line = fgets($fh); $chr = explode("\t",$line); if ((int)$chr[sizeof($chr)-1] >= $overlaps) // according to some criteria { //print "$chr $overlaps"; fwrite($fh1,$line); } } fclose($fh); fclose($fh1); } ###############overlap_bedfile(overlap interval)################ $new_file1 = "temp/$random_number"."_overlapbedfile".".txt"; // overlap_bedfile $fh =fopen($new_file,"r") or exit("Unable to open $new_file!"); // read from an original overlapped file, $temp $fh1=fopen($new_file1,"w") or exit("Unable to write $new_file1!"); // write into a new overlapped file while(!feof($fh)) { $line = fgets($fh); $chr = explode("\t",$line); for ( $i=1; $i<=sizeof($chr)-1; $i++) { if ($chr[$i] == $chr[0]) { $i += 1; $low = max($chr[$i], $chr[1]); // low boundary of the overlap interval $high = min($chr[$i+1],$chr[2]); // high boundary of the overlap interval fwrite($fh1,"$chr[0]\t$low\t$high\n"); } } } fclose($fh); fclose($fh1); system("chmod a+x 777 $new_file"); system("chmod a+x 777 $new_file1"); #################### Plot Graphics ####################### $chromosome = chromosome_count($new_file); $fmt_xaxis = join("|",array_keys($chromosome)); $fmt_yaxis = join(",",array_values($chromosome)); //cht (chart type), chd (data), and chs (chart size) //print max(array_values($chromosome)); $chart1 = "