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

my %whole_pedigree;

open( my $in, '<', 'wholepedigree_F.txt');
while ( my $line = <$in> ) {
    chomp $line;
    my ( $ID, $sire, $dam, $F, $FB, $AHC, $FA ) = split ( /\s+/, $line );
    if ( $ID ) {
        $whole_pedigree{ $ID } = "$F\t$AHC";
    }
}
close $in;

open( my $look_for, '<', 'damF.txt' );
open( my $output,   '>', 'output.txt' );

while ( my $line = <$look_for> ) {
    chomp $line;
    my ( $damID, $damF, $damAHC, $prog ) = split (/\s+/, $line);
    if ( $prog && $whole_pedigree{ $prog } ) {
         print $output join( "\t", $prog, $whole_pedigree{ $prog }, "$damID\t$damF\t$damAHC" ), "\n";
    }
}
close $look_for;
close $output;

print "Done\n";

##</code><code>##

cat output.txt 

##</code><code>##

3162	0	0	501093	0	0
3163	0	0	2958	0	0
3164	0	0	1895	0	0
3165	0	0	1382	0	0
3166	0	0	2869	0	0