Ignoring moritz's very good suggestion, you could perform a naive search by storing the contents of the first file in an array of arrays. This would end up looking something like (untested): 

my @file1 = ();
open(FILE, @ARGV[0]) || 
    die ("could not open file @ARGV[0]\n");

    while (my $line = <FILE>) {
    chomp $line;
    my ($chr, $start, $stop) = split(/\t/, $line);
        push @file1, [$chr, $start, $stop];
    }
close FILE;

open(FILE, @ARGV[1])||die ("could not open file @ARGV[1]\n");
    
    while(<FILE>){
        ($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB)= s
+plit;        
#        foreach (line in genes.db){   # I don't know what to put here
+.
        foreach my $line (@file1){
            my ($chr, $start, $stop) = @$line;
            if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModE
+nd){
            $Count++;
            print ;($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,
+$SizeKB,$Count)
            }    
    }

[download]

Note that your original concept had some scoping issues.

In reply to Re: Searching and Coutning using 2 files with multiple columns by kennethk
in thread Searching and Coutning using 2 files with multiple columns by shart3

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