This is tested and works, assuming the format is the same as what you said (just a single line of numbers separated by commas in each file). You'll need to change the path for opening files, though, and if this is for homework (which seems likely), you'll want to rewrite the code and make sure you understand all of it.

use strict;
use warnings;
use Data::Dumper;

my $tree = build(1);
print Dumper($tree);

my @arr = traverse($tree);
print "@arr";

sub traverse {
    my $p = $_[0];
    return ($p->{'key'}, map { traverse($_) } @{$p->{'branches'}});
}

sub build {
    my (%node, $key, @branches, $handle);
    $key = $_[0];
    $node{'key'} = $key;
    $node{'branches'} = \@branches;
    if (open ($handle, "$key.txt")) {
        chomp($_ = join '', <$handle>);
        close($handle);
        for (split /,/, $_) {
            push @branches, build($_);
        }
    }
    return \%node;
}
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