Get everything working, extract line by line in BED file, run hgWiggle and calculate conserved bases and conserved regions and output into bed file

conservation2.pl

#!/usr/bin/perl -w
 

 
my $numb = 1;
open(RefGenes, "< ../RefGenes.bed");
while(<RefGenes>)
 {
 
 print("$numb\r");
 
 # Good practice to store $_ value because
 # subsequent operations may change it.
 my($line) = $_;
  
 # Good practice to always strip the trailing
 # newline from the line.
 chomp($line);

 # Convert the line to upper case.
 #$line =~ tr/[a-z]/[A-Z]/;

 # Print the line to the screen and add a newline
 
 my @data = split(/\t/, $line);
 getCoverage($data[0],$data[1],$data[2]);
 $numb++;
 } 

close (RefGenes);



sub getCoverage {
    ($chr, $start, $end) = @_;

#/nfshomes/aniba/bin/x86_64/hgWiggle -chr=chr12 -position=chr12:51987539-51987559 -rawDataOut  phastCons44way > tmp

    @score = `/nfshomes/aniba/bin/x86_64/hgWiggle -chr=$chr -position=$chr:$start-$end -rawDataOut phastCons44way > tmp`;
#print "RawData/bigWigSummary $bwfile $chr $start $end $step 2>&1";
    system(@score);
    #print(@RCMD);
    @RCMD = `R CMD BATCH --no-save --no-restore '--args $chr $start $end' coveragecount.R`;
system(@RCMD);

}