Hi Monks, So I know many monks here aren't biologist but I have posted my question on bioinfo forums aswell but haven't been able to solve the issue. Since it involves perl I thought maybe you all will be able to point out something in the code. My question, I am trying to find overlap between CNV(a variant basically) which has genomic region(start and stop basepair position), eg: 23487 72875 and genes which also have this (start and stop bp position) eg: BRCA1 41196312 41277500. Overlap can be in different ways: i). either there wont be any overlap i.e the gene region will not fall in the CNV region or ii). it will fall completely within the region or iii) it may fall partially i.e gene region might overlap with the CNV start position or gene region overlapping with the stop postion of the CNV. So if there will be an overlap it will return 1 and if not then it will return 0 and the output file finally will have all the overlap and the gene name with which this cnv region is overlapping. So I am reading in the main CNV file and two other gene list files. Three tab delim files I have are 
file1=cnv file
start   stop  size(in bp) 
5389769  98256008  3567
7452344  871875466 64547

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

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

[download]
note: I cannot merge the two gene lists as they are different sets and need to be kept separate. Am I doing this correctly? Any suggestions? 
 !/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);

[download]
I get a blank output file. There is no error or warning that I am getting so I am not sure what is going on and what I should be correcting? My output file should be if overlapping regions found 
gene name  size  start stop 
xyz         5464 83654272 6735353
...
...

[download]

In reply to overlapping regions by perllearner007

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