while (<FILE2>) {
  push @col, $_ =~ m/^(\S+)/  unless ...;
}

##</code><code>##

while(<COL>) {
  $_ =~ s/^(\S)/$1 $col[$i++]/;
  print OUT2 $_;
}

##</code><code>##

while (<COUNT>){
  ($i, $j) = ...


##</code><code>##

my ($i, $j)

##</code><code>##

open (FILE, "test.pat") or die "Can't open test.pat: $!";
open (OUT, ">TRUE_OUTPUTS") or die "Can't open TRUE_OUTPUTS: $!";
while (<FILE>) {
  if ($_ =~ m/^\s{4,}(\d)\s+$/) {print OUT "$1\n"}
}
close (FILE);
close (OUT);