I don't really understand what in FILE2 is supposed to match with what in FILE1? All non-zero data in FILE1 is in some column in FILE2. You do not show a line in FILE2 that would not "match" and you do not provide a sample "good" output.

I started re-writing your code, but could not proceed to a final solution due to the above. However this code below may help you.

Some comments to your code:

• "use vars" does not do what you think and there is absolutely no need for that here.
• I only see the need for a single hash of FILE1 - a second hash is not necessary.
• I have no idea about what you think this $N stuff does?
• There is no need for a multi-dimensional hash here and your syntax to address a simple hash is wrong (don't need the arrows).

#!/usr/bin/perl
use warnings;
use strict;
use diagnostics;

my %hash;

#$damID, $damF, $damAHC, $prog
my $damF = <<END;
501093    0    0    3162
2958    0    0    3163
1895    0    0    3164
1382    0    0    3165
2869    0    0    3166
END

#$ID, $sire, $dam, $F, $FB, $AHC, $FA
my $wholepedigree_F = <<END;
3162    2159    501093    0    0    0    0
3163    2960    2958    0    0    0    0
3164    2269    1895    0    0    0    0
3165    1393    1382    0    0    0    0
3166    2881    2869    0    0    0    0
END


open (FILE1, '<', \$wholepedigree_F) or die "Couldn't open wholepedigr
+ee_F.txt";

while (my $line = <FILE1>)
{
    chomp $line;
    next unless $line =~ /\S/; #skip blank lines
    
    my ($ID, $F, $AHC) = (split (/\s+/, $line))[0,3,5]; 
    $hash{$ID} = "$F\t$AHC"; 
}
close FILE1;

open (FILE2, '<', \$damF) or die "Can't open damF.txt";
#open (OUT, ">output.txt") or die "Can't Open output file";
#print OUT "\n"; 

while (my $line = <FILE2>) 
{
    chomp $line;
    next unless $line =~ /\S/; #skip blank lines
    my ($damID, $damF, $damAHC, $prog) = split (/\s+/, $line); 
    
    if ($hash{$prog})
    {
       my $info1 = $hash{$prog};
       my $info2 = "$damID\t$damF\t$damAHC";
       print "$prog\t$info1\t$info2\n";
    }
}

#close OUT;
close FILE2;
print "Done";
[download]