for (@resultarray) { s/^0$/1/ };

for(my $i = 0; $i < $originalfilecount; $i++)
        {
            if($first)
            {
                $first = 0;
                
                #print OUT5 "\t$resultarray[3]";
                $outputb = "\t$resultarray[3]";
            }
}

        #print OUT5 "\n";
        
            push(@output5a, $outputa);
            push(@output5b, $outputb);
           
           for(@output5b){s/0/1/g}; #convert output from 0 to 1
[download]

... how do I substitute the $resultarray[3] values from 0 to 1 instead of doing at @resultarray?

One way:

>perl -wMstrict -le
"use Data::Dump;
 ;;
 my @resultarray = (0, 0, 0, 0, 0, 0);
 dd \@resultarray;
 ;;
 $resultarray[3] =~ s/^0$/1/;
 dd \@resultarray;
"
[0, 0, 0, 0, 0, 0]

[0, 0, 0, 1, 0, 0]
[download]

Your problem is almost certainly this line:

$outputb = "\t$resultarray[3]";
[download]

$outputb does not equal $resultarray[3]; it equals a TAB ('\t') followed by $resultarray[3].

Here's some examples of the types of tests you could have run to check this yourself:

#!/usr/bin/env perl -l

use strict;
use warnings;

my @resultarray;
my $outputb;

$resultarray[3] = 0;
$outputb = "\t$resultarray[3]";

print '$resultarray[3] = |', $resultarray[3], '|';
print '$outputb = |', $outputb, '|';

check_for_match_zero('$resultarray[3]', $resultarray[3]);
check_for_match_zero('$outputb', $outputb);

sub check_for_match_zero {
    my ($name, $value) = @_;

    if ($value =~ /^0$/) {
        print "$name (with value: '$value') MATCHES zero.";
    }
    else {
        print "$name (with value: '$value') DOES NOT MATCH zero.";
    }
}
[download]

Output:

$resultarray[3] = |0|
$outputb = |    0|
$resultarray[3] (with value: '0') MATCHES zero.
$outputb (with value: '    0') DOES NOT MATCH zero.
[download]

[I see ++AnomalousMonk has shown you how to do the substitution on just one element (i.e. $resultarray[3]) as requested.]

-- Ken