Good Morning Monks,

I have a problem that I could do rather easily in Excel, but my files are too large, and I can't seem to figure out a way for perl to do it, although I know it can.

I have two files Boundary.out and DB.out. Boundary.out look like this:

chr1    3204562    3661779
chr1    4334223    4350673
chr1    4481008    4486694
chr1    4764014    4775968
chr1    4797773    4836816
chr1    4847574    4887987
chr1    4847574    4887987
chr1    4848208    4887987
chr1    4900049    5009660
chr1    5073053    5152630
[download]

and DB.out looks like this:

Xkr4    chr1    3204562    3661779    -    3    457.217
Rp1    chr1    4334223    4350673    -    4    16.45
Sox17    chr1    4481008    4486694    -    5    5.686
Mrpl15    chr1    4764014    4775968    -    5    11.954
Lypla1    chr1    4797773    4836816    +    9    39.043
Tcea1    chr1    4847574    4887987    +    10    40.413
Tcea1    chr1    4848208    4887987    +    10    39.779
Rgs20    chr1    4900049    5009660    -    5    109.611
[download]

for each row in DB.out I want to count the number of times that a row in Boundary.out occurs where column 0 in Boundary.out eq col1 in DB.out AND col1(Boundary) gt col2(DB) AND col2(Boundary)lt col3(DB). That value should be added to col7(DB).

Here is what I have so far:

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);
    }
close FILE;

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

Can anyone help????????????