"; print "File1: ".$file1; print "
"; print "File2: ".$file2; print "
"; $split_file1 = preg_split('[/|\.]',$file1,-1,PREG_SPLIT_OFFSET_CAPTURE); $split_file2 = preg_split('[/|\.]',$file2,-1,PREG_SPLIT_OFFSET_CAPTURE); $split_file1[sizeof($split_file1)-2][0]; $split_file2[sizeof($split_file2)-2][0]; $temp = "temp.bed"; $action = "/var/www/DASR_2011/BEDTools-Version-2.11.2/bin/intersectBed -wao -a $file1 -b $file2 >$temp"; // $temp, original overlapped file system($action); // call BEDTools $new_file = $split_file1[sizeof($split_file1)-2][0]."_AND_".$split_file2[sizeof($split_file2)-2][0].".bed"; // create a new file name overlaps_cut($new_file,$temp,$overlaps); //**********************get cutoff processed file function overlaps_cut($new_file,$temp,$overlaps) { $fh =fopen($temp,"r") or exit("Unable to open file!"); // read from an original overlapped file, $temp $fh1=fopen($new_file,"w") or exit("Unable to write 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($fh1); } //**********************plot plot($new_file); print "
Figure 1: Overlap-counts distribute on all Chromosome.
"; plot_percentage($new_file,$file1); print "
Figure 2: Overlap-percentage on all Chromosomes of ".$split_file1[sizeof($split_file1)-2][0]."
"; plot_percentage($new_file,$file2); print "
Figure 3: Overlap-percentage on all Chromosomes of ".$split_file2[sizeof($split_file2)-2][0]."
"; print "