file1=cnv file
start   stop  size(in bp) 
5389769  98256008  3567
7452344  871875466 64547

##</code><code>##

file2=genelist1
name start stop
BRCA1 41196312   41277500
TP53   7571720    7590863

##</code><code>##

file3=genelist3
name start stop
OMG  29621668   29624380
NR3C1  142657496..142815077

##</code><code>##

 !/usr/bin/perl
    
    #Open the cnv file with start, stop 
    
    my $input_gene_file = "path to file";
    die "Cannot open $input_gene_file\n" unless (open(IN, $input_gene_file));
    
    my %size_CNV_start_CNV_stop;
    while (chomp($line = <IN>))
    {
    	my (@columns) = split /\s+/, $line;
    	my $size = $columns[3];
            my $CNV_start = $columns[1];
    	my $CNV_stop = $columns[2];
            $size_and_CNV_start{$size} = $CNV_start;
            $size_and_CNV_stop{$size} = $CNV_stop;
    }
    close(IN);
    	
    #Now open files for genelist1 and genelist2 with respective start and stops
    
   open (MYFILE, "/Users/pathtofile");
@file1 = <MYFILE>;
close MYFILE;
open (MYFILE2, "/Users/pathtofile");
@file2 = <MYFILE2>;
close MYFILE2;

#Open output file and write the locations/position of each symbol
die "output.txt" unless(open( OUT,"> output.txt"));


while(defined(my $line1 = <$file1>)
        and defined(my $line2 = <$file2>)){
    
   
    sub overlap {
    	my ($CNV_start, $CNV_stop, $Gene_start, $Gene_stop) = @_;
         if ($Gene_stop < $CNV_start || $Gene_start < $CNV_stop) {
    return 0;
        if (Gene_stop > $CNV_start || $Gene_stop > $CNV_stop){
    }
    return 1;
    }
    
    
    
    
    
    while (defined($symbol = <IN>))
    {
     chomp($symbol);
    {
     
    	my $CNV_start = $size_and_CNV_start{$size};
    	my $CNV_stop = $size_and_CNV_stop{$size};
            print OUT " $name\ $size\ $CNV_start\ $CNV_stop \n";
    }
    }
    }
    close(OUT);


##</code><code>##

gene name  size  start stop 
xyz         5464 83654272 6735353
...
...