Hi Athanasius, Hope you are well and thank you for all of your help so far. Unfortunately I still have not been able to get the code working as I want it to and I was hoping you could have one further look at the code I am running. The format of my input files has changed slightly but I don't think this will affect the code too much. 

File 1
CHROM    POS    REF    ALT    VARIANT_LIST    209T-D  459T-D    644T-D
+    94T-D    99T1-D    99T2-D    99T3-D    99T4-D    99T5-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', '
+A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'T', 'T', 'T', 'T', 'T', 'T'
+, 'T']
...

[download]
File 2 
CHROM     POS     REF     ALT     VARIANT_LIST    209H-D    459H-D    
+644H-D    94H-D    99H-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'REF', 'REF', 'REF', 'REF']
['MT', '2962', 'C', 'T', 'T', 'REF', 'REF', 'T', 'REF', 'T']
....

[download]
Again I want to compare 99T1, 99T2, 99T3, 99T4 and 99T5 of File1 with 99H of file 2. The output I want looks like 
 
CHROM    POS    REF    ALT    VARIANT_LIST    209T-D  459T-D    644T-D
+    94T-D    99T1-D    99T2-D    99T3-D    99T4-D    99T5-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', '
+A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'REF, 'T', 'REF', 'REF', 'RE
+F', 'REF', 'REF']

[download]
(because the same letter at the same position in File 1 and File 2 should output REF, and if REF is found at that position in file 2, just output letter from File 1) The code I am currently running is: 
#!/usr/local/bin/perl 
use strict;
use warnings;

my $file1 = shift;
my $file2 = shift;

open(my $in1, '<', $file1)
    or die "Cannot open file '$file1' for reading: $!";

open(my $in2, '<', $file2)
    or die "Cannot open file '$file2' for reading: $!";

my $header1 = <$in1>;
<$in2>;
my @heads1  = split "\t", $header1;
my $index = 5;
my %index_map;

for (@heads1)
{
    $index_map{$index++} = $1 + 4 if m/^(\d+)/;
}

print $header1;
while (my $line1 = <$in1>)
{
    my @fields1 = get_fields($line1);

    defined(my $line2 = <$in2>)
        or die "Data missing in file '$file2': $!";

    my @fields2 = get_fields($line2);
    my @out     = @fields1;

 for my $i (5 .. $#fields1)
    {
    my $j = $index_map{$i};
        
    if ($fields1[$i] ne 'REF')
            {
        
            $out[$i] = $fields2[$j] if exists $fields2[$j] &&
                        $fields2[$j] ne 'REF';

        }

}
    @out = map { "'$_'" } @out;
    print '[', join(', ', @out), "]\n";
}

close $in2
    or die "Cannot close file '$file2': $!";

close $in1
    or die "Cannot close file '$file1': $!";

sub get_fields
{
    my ($line) = @_;

    chomp $line;
    my @fields = split "\t", $line;
    s{ ^ \[? ' }{}x for @fields;
    s{ ' \]? $ }{}x for @fields;

    return @fields;
}

[download]
which should work but the output is 
CHROM    POS    REF    ALT    VARIANT_LIST    209T-D  459T-D    644T-D
+    94T-D    99T1-D    99T2-D    99T3-D    99T4-D    99T5-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', '
+A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'T', 'T', 'T', 'T', 'T', 'T'
+, 'T']
...

[download]
I really do not know what is going wrong? If you have any suggestions please let me know. Thanks!

In reply to Re^4: Can't access data stored in Hash - help! by corcra
in thread Can't access data stored in Hash - help! by corcra

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