Hi everyone, I am trying to merge common values between two files and print out the relevant information. I am using a code I have used many times to merge files, and for some reason it isn't working. There seems to be a problem with calling out the first hash in the second part of the script- but it should work with the global variables declared. The format of the input files are: damF.txt

501093    0    0    3162
2958    0    0    3163
1895    0    0    3164
1382    0    0    3165
2869    0    0    3166
[download]

wholepedigree_F.txt

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
[download]

I want the output to match column 4 of damF.txt and wholepedigree_F.txt and print columns 3 and 5 of whole_pedigree and columns 1,2,3 of damF.txt. this is the code:

#!/usr/bin/perl
use warnings;
use strict;
use diagnostics;
use vars qw($ID $sire $dam $F $AHC $FB $FA $hash1 %hash1 $info1 $damID
+ $damF $damAHC $prog $hash2 %hash2 $info2);

open (FILE1, "<wholepedigree_F.txt") or die "Couldn't open wholepedigr
+ee_F.txt\n";
my $N = 1; 
while (<FILE1>){
    chomp (my $line=$_);
    next if 1..$N==$.; 
    my ($ID, $sire, $dam, $F, $FB, $AHC, $FA) = split (/\t/, $line); 
    if ($ID){
    $hash1 -> {$ID} -> {info1} = "$F\t$AHC"; 

}
}

close FILE1;
open (FILE2, "<damF.txt") or die "Can't open damF.txt \n";
open (Output, ">output.txt") or die "Can't Open output file";
print Output "\n"; 

while (<FILE2>) {
    chomp (my $line=$_);
    next if 1..$N==$.; 
    my ($damID, $damF, $damAHC, $prog) = split (/\t/, $line); 
    if ($prog){
    $hash2 -> {$prog} -> {info2} = "$damID\t$damF\t$damAHC"; 
    }
     if ($prog && ($hash1->{$ID})) {
    $info1 = $hash1 -> {$ID} -> {info1};
    $info2 = $hash2 -> {$prog} -> {info2};
    print "$ID\t$info1\t$info2\n";
}
}

close Output;
close FILE2;
print "Done";
[download]

Please note that the input files have about 500000 entries in each column. Please help! Thanks in advance!

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